R&D Tax Relief Software Issues: How To Avoid Delays With CT600L Claims

If you are still waiting on an R&D tax credit repayment from HMRC, the issue may not always be the R&D activity itself. In many cases, delays start at the filing stage, especially where the CT600L supplementary page, Additional Information Form, tax computation and company return do not match.

A wrongly populated box, an outdated software version, missing bank details or inconsistent figures can move a claim into manual review. That can slow down repayment and increase the chance of HMRC asking further questions.

This article walks you through what to check before you submit, what to fix if something has already gone wrong, and what to do if your claim has stalled. The advice applies whether you are claiming under the UK merged scheme, the older RDEC rules for accounting periods before 1 April 2024, or the Irish R&D tax credit if you operate on both sides of the border.

Why the CT600L causes more friction than you might expect

HMRC introduced the CT600L from 1 April 2021 as a supplementary page to the main CT600. The form captures the detailed mechanics of an R&D claim, particularly under the Research and Development Expenditure Credit route and the newer merged scheme.

Before CT600L was introduced, many claims were summarised in fewer boxes on the main CT600. The supplementary page now asks for more detailed information, including expenditure credit calculations, PAYE and National Insurance cap details, and how the credit is being used or surrendered.

That detail is useful, but it also creates more room for error. Every additional box is another place where software can populate the wrong figure, validation can fail, or the figures can fall out of step with the accounts, tax computation or Additional Information Form.

Tax software issues with the CT600 family of forms are not new. HMRC publishes updates on GOV.UK about changes and issues affecting the Corporation Tax online service, including CT600 and CT600L changes. The 2026 version of CT600L reflects the merged scheme and enhanced R&D-intensive support rules, so businesses filing under the newer regime need to be especially careful.

If you are claiming under the merged scheme for the first time, you may be using parts of the form that are still unfamiliar to your team or adviser. That is worth knowing before assuming a delayed repayment means the claim itself is weak. Our piece on common mistakes businesses make when claiming R&D tax relief covers the wider issues, beyond the mechanical filing problems, that materially raise the risk of an HMRC enquiry.

The categories of CT600L issues to look for first

The technical problems usually fall into a small number of categories. Once you understand them, you can often spot the likely cause of a delay before HMRC writes to you.

These are the issues that most often create problems:

• Boxes left blank where a zero is needed. Some software may allow a blank value where HMRC’s system expects an actual figure.
• Validation failures around brought-forward amounts. Carry-forward figures in RDEC-style calculations can create filing problems if they are not carried across correctly.
• PAYE and National Insurance cap boxes. These need to be completed carefully where the cap applies or where a company is relying on an exemption.
• iXBRL and computation mismatches. HMRC can compare the accounts, computation, CT600 and CT600L. Inconsistent figures can trigger questions.
• Bank details missing on the CT600. If bank details are missing, HMRC may not be able to make a repayment by BACS, which can delay payment.
• Software versions that pre-date HMRC’s latest updates. If your provider has not pushed the latest release, you may still be filing against outdated validation rules.

If any of those look familiar from a recent return, that may explain the delay. Our digital bookkeeping team often picks up these issues when reviewing client records before a claim goes out, and the fix is usually quicker than people expect.

How long should you actually be waiting?

HMRC’s published aim has been to process 85% of R&D tax credit claims within 40 working days. In practice, processing times vary depending on claim quality, scheme type, filing volumes and whether the claim is selected for further checks.

The realistic picture in 2026 looks like this:

Most well-prepared claims under the merged scheme are likely to take longer than the old expectation of a few weeks. A clean older SME claim filed at a quiet point in the cycle can still complete faster. Anything that triggers a compliance check should be planned for as a much longer process.

For broader context on how the deadline framework around Corporation Tax filings fits together, our self-assessment tax returns guide covers the parallel pressures on directors who also file personally.

The April 2024 merged scheme is still bedding in

For accounting periods beginning on or after 1 April 2024, the old SME and RDEC schemes were replaced by a single merged R&D expenditure credit scheme, with a separate enhanced R&D-intensive support route for loss-making SMEs where qualifying R&D expenditure is at least 30% of total expenditure.

The merged scheme uses RDEC-style mechanics for most companies. That means more businesses are now using the CT600L in detail. The change has surfaced practical issues that many SMEs did not previously face, because older SME claims often relied more heavily on the main CT600 rather than a full expenditure credit calculation.

If your first claim under the merged scheme is also your first time using CT600L in detail, that combination can explain some of the friction you may be seeing.

If you are not yet sure your activity qualifies in the first place, our piece on what qualifies for R&D tax credits in the UK and Ireland is the right place to start before worrying about the form. Our companion piece on the UK and Ireland R&D tax credit landscape walks through the sector-by-sector activity types that qualify, which is useful if you are uncertain whether your work fits.

The merged scheme is also pulling more attention onto other related reliefs. Land remediation relief and the wider business owner’s guide to capital allowances cover reliefs that often sit alongside an R&D position, particularly for manufacturing, engineering and property-active businesses.

Practical steps to avoid a delayed claim

You cannot control HMRC’s processing speed, but you can reduce the chances of your claim being slowed down by avoidable errors. The checks below are the same ones our specialist tax team runs before any CT600L goes out.

Run through these before you submit:

• Confirm your filing software is on the latest HMRC schema. Most commercial providers issue updates ahead of HMRC’s annual changes. If your software has not been updated recently, stop and update it.
• Cross-check every CT600L box against the Additional Information Form. HMRC introduced the AIF requirement for most R&D claims from 8 August 2023. Figures should reconcile across the AIF, CT600, CT600L and computation.
• Populate the company bank details on the CT600. This is one of the simplest fixes and can help avoid repayment delays.
• Avoid filing in peak periods where possible. Heavy filing months can lead to longer processing times.
• Keep the technical narrative tight and project-led. HMRC reviews the narrative against the financial detail. Vague descriptions of “improving processes” without identifying the specific scientific or technological uncertainty are more likely to be challenged.
• Show the PAYE and National Insurance cap calculation if it applies. If you are claiming an exemption, keep evidence supporting why the exemption applies.

A claim that does all of the above is much easier to defend if HMRC asks questions. Our pieces on how tax accountants help small businesses and why internal audit supports business growth both touch on the underlying habit that makes R&D claims easier: keeping clean, current records rather than reconstructing them at year-end.

What to do if your claim is already stuck

If your CT600L claim has been sitting longer than expected without any contact from HMRC, the position is not automatically bad. It may simply be in a manual review queue. It is also the point where you should start taking action rather than waiting indefinitely.

Take these steps in order:

• Confirm the claim was actually received. Your filing software should have stored a submission receipt. Without it, HMRC may not have the claim at all.
• Check the company’s Corporation Tax online account. Updates and HMRC correspondence may appear there before they arrive in the post.
• Review the AIF, CT600, CT600L and computation together. Look for mismatched expenditure totals, incorrect scheme selection and missing bank details.
• Contact HMRC through the appropriate Corporation Tax or R&D channel if the claim is significantly overdue.
• If a compliance check letter has arrived, do not ignore it. Non-response can lead to the claim being reduced or refused. Engage with the questions in writing, with full supporting detail.

If a compliance check turns into a full enquiry, specialist support becomes more valuable. The standard of evidence required is higher, and time pressures are real. Where the underlying numbers themselves come into dispute, forensics accountants with experience of expert witness work can help present the financial picture in a form that withstands HMRC scrutiny. Our pieces on how forensic accounting helps in fraud investigations and forensic accounting vs audit explain where this kind of work fits.

Cross-border claims add another layer

If your business operates on both sides of the UK to Ireland border, your R&D position rarely sits neatly in one jurisdiction. You may have qualifying activity in Northern Ireland under UK rules, and parallel activity in the Republic under the Irish R&D tax credit regime.

For accounting periods commencing on or after 1 January 2024, the Irish R&D tax credit rate is 30%. Ireland has also legislated for a 35% rate for later periods, so businesses with longer-term R&D planning should keep the timing of Irish claims under review. The rules around subcontracted R&D, group structures and where costs are incurred differ between the UK and Irish regimes.

You cannot claim the same cost twice. You can, in many cases, claim related but distinct costs under each scheme, depending on where the work is done and who incurs the expense. The interaction needs to be planned before either return is filed.

This is where good Cross-border tax advisory support pays for itself. Our team works regularly with manufacturing, engineering and technology businesses that have R&D activity in both jurisdictions, and the cross-border view changes how each individual claim is built. Our article on VAT compliance for businesses operating across the UK to Ireland border covers the wider compliance picture for businesses in this position, and our piece on cross-border payroll does the same for staffing. For groups thinking about a more structural dual presence, setting up a company in both the UK and Ireland is a useful starting point.

A quick comparison of the R&D routes

Here is how the main UK R&D options compare for accounting periods beginning on or after 1 April 2024, alongside the Irish credit:

The form you should be filing depends entirely on your accounting period and which scheme applies. Filing against the wrong scheme is itself a common cause of delay.

What HMRC compliance activity looks like right now

HMRC has expanded its compliance activity around R&D claims since 2022 in response to error, fraud and inflated claims. The shift from “process now, ask later” to a more cautious review environment is now well established, and businesses should expect more questions where a claim is unclear, inconsistent or poorly evidenced.

In practice, this means more enquiries, more requests for additional information and more claims being reduced or rejected where the evidence does not support the figures. The criteria HMRC uses to assess risk are not fully published, so the safest approach is to assume that every claim should be capable of standing up to detailed review.

If a claim becomes contentious and the wider financial position comes into dispute, the case for involving experienced chartered accountants Northern Ireland businesses can rely on becomes stronger. Our pieces on red flags of financial fraud in SMEs and what a forensic accountant does and when you need one cover the kinds of issues that can surface when an enquiry escalates. Where pressure on cash becomes acute during a delay, our recovery accounts UK team can also help you stabilise the position, and our article on how recovery accountants help improve cash flow explains the practical side of that.

Watch the wider tax landscape too

R&D is rarely the only thing happening at the same time. Recent and upcoming UK changes are worth keeping in view because they affect cash flow and timing decisions around your claim:

• The merged scheme rules continue to apply for accounting periods beginning on or after 1 April 2024.
• From 1 April 2026 for Corporation Tax, the main rate of writing down allowance for plant and machinery reduced from 18% to 14%, which slows the rate at which some qualifying expenditure generates relief.
• Dividend tax rates increased from 6 April 2026 for the ordinary and upper dividend rates.
• Making Tax Digital for Income Tax now applies in phases, starting with sole traders and landlords with qualifying income over £50,000.
• HMRC confirmed in July 2025 that Making Tax Digital for Corporation Tax will not proceed.

If you need the broader picture, our piece on Making Tax Digital and what UK and Irish businesses need to know and our companion guide Making Tax Digital explained together cover the wider shifts. For payroll-related changes, HMRC PAYE issues and the salary sacrifice pension changes pieces are worth reading. For longer-term thinking, our piece on the future of financial planning and tax planning for UK businesses expanding overseas sit naturally alongside an R&D conversation.

Where SCC fits in

SCC Chartered Accountants’ specialist tax team prepares R&D claims for businesses across Northern Ireland, the Republic and the wider UK. Our work spans the merged scheme, ERIS, RDEC, the Irish credit and the cross-border interactions between them. We prepare and review the supporting Additional Information Form and the technical narrative, both of which now matter as much as the CT600L itself.

If you are a manufacturing, engineering, software, food or construction business, you are in the sectors where qualifying activity is often broader than business owners realise. Our SME business solutions team works closely with the specialist tax team to make sure the wider business context, including cash flow, working capital and growth plans, is reflected in how the claim is approached. Our tax compliance service covers the surrounding obligations, and our corporate finance work supports the businesses for whom R&D is one part of a wider growth or transaction story.

For owner-managers thinking about the broader picture, the key financial KPIs every SME owner should be monitoring monthly, how management accounts help SME owners and switching to cloud accounting for SMEs cover the operational disciplines that make R&D record-keeping easier in the first place.

FAQs

How long does HMRC take to process a CT600L claim?

HMRC’s published aim has been to process 85% of R&D claims within 40 working days of receipt. In practice, claims under the merged scheme can take longer, especially if HMRC needs to review the claim manually or ask further questions. A clean older SME claim may complete more quickly, while anything subject to a compliance check should be planned for as a longer process.

What is the CT600L supplementary form?

The CT600L is a supplementary page to the main CT600 Corporation Tax return. It captures the detailed financial mechanics of an R&D claim, particularly expenditure credit calculations, PAYE and National Insurance cap details, and how the credit is being used, surrendered or repaid.

Do I need to file a CT600L for the new merged R&D scheme?

Yes, claims under the merged R&D expenditure credit scheme generally require the CT600L, alongside the CT600 and Additional Information Form. The exact filing requirements depend on the accounting period, scheme and type of claim being made.

Why is my R&D repayment delayed?

Common causes include software validation failures, missing or inconsistent figures across the CT600, CT600L, AIF and computation, missing bank details for BACS payment, filing during busy periods and selection for a compliance check. The first few are within your control. A clean filing reduces avoidable delay and makes the claim easier to defend.

Can I file the CT600L on paper if my software fails?

In exceptional cases HMRC may accept a paper CT600 return where a known online filing issue prevents submission. This is generally a last resort. For most businesses, the better first step is to update the software, check the return against HMRC’s current requirements and file electronically where possible.

What happens if HMRC opens an enquiry into my R&D claim?

You will receive a compliance check letter setting out the questions. You should respond in writing, with full technical and financial detail, within the deadline given. Ignoring the letter can lead to your claim being reduced or rejected. Specialist support at this stage is usually worth the investment.

Can I claim R&D tax relief in both the UK and Ireland?

If you have qualifying R&D activity in both jurisdictions, you may be able to claim under each scheme. You cannot claim the same costs twice. The interaction requires careful planning, particularly around subcontracted work, group cost allocations and where the work is actually carried out. Our piece on common tax mistakes expats and cross-border businesses make touches on related cross-jurisdiction pitfalls.

Get the right support in place

If your CT600L claim is delayed, or you want to file your next one without the same problem, this is the kind of work our team does every week. As accountants Armagh businesses, cross-border firms and UK-wide clients turn to, we combine genuine R&D specialism with deep knowledge of the wider tax position, so your claim is built to stand up to HMRC scrutiny.

Contact the SCC Chartered Accountants team for a straightforward review of your current or upcoming R&D claim, including the CT600L position, the supporting evidence and the wider tax landscape it sits within.