Calling Frustrated Accountants: HMRC RTI Issues Are More Than Just Payroll Glitches - Here's What You Need to Know
- austin3133
- Apr 8
- 4 min read
If your clients have ever come to you confused about unexpected HMRC charges, mismatched PAYE records, or employee tax code chaos, the problem may not be with their payroll provider, or even with the data they’ve submitted.
According to a recent report by the Chartered Institute of Payroll Professionals (CIPP), there are systemic issues within HMRC’s Real Time Information (RTI) system that are leaving both agents and employers stuck in a cycle of errors, disputes, and long delays.
This is something accountants need to be aware of, because it’s often you who clients turn to when they’re trying to make sense of their PAYE accounts or when letters from HMRC start landing on their desks.
So, what’s going wrong with RTI?
The CIPP report highlights a number of recurring and deeply rooted issues that are creating serious pain points for businesses:
RTI submissions are not always correctly allocated to employer records, despite being accepted.
Backlogs in the Charge Resolution Team (CRT) mean cases can remain unresolved for over 12–36 months.
Helpline staff lack access to full RTI records, meaning accountants or agents can get stuck in circular conversations.
Incorrect tax codes are being issued based on flawed data, often requiring individual employees to call HMRC directly.
Amended FPS submissions - the supposed “fix” - don’t always work or get applied properly.
These aren’t one-off teething problems. They’re systemic, and they’re affecting businesses of all sizes, including large NHS trusts and companies with impeccable submission histories.
What this means for accountants
As an accountant, you’re not just watching the numbers — you're also managing client expectations and reputations. These RTI problems often land in your lap with little warning and even less clarity. Here’s how they could be affecting your practice:
Unexpected time drain – Chasing HMRC, investigating discrepancies, and explaining problems to confused clients eats into your fee-earning time.
Client trust on the line – When tax codes are wrong or liabilities appear out of nowhere, your clients look to you for answers. It's a tough spot if HMRC isn't being transparent.
Limited visibility – Without access to the RTI data held by HMRC, you’re left second-guessing what’s been submitted and processed.
Cash flow complications – Clients may be pressured into paying disputed amounts to avoid legal action, even when they don’t owe the money.
This is particularly frustrating when you’ve done everything right — submitted correct data, used compliant software, and still ended up with a charge on the account.
Case in point
The CIPP included several real-world case studies, including:
A company where failed RTI submissions still partially processed employee data, resulting in multiple salaries showing on HMRC’s side — but not in reality.
A business going through administration that submitted final payrolls correctly, only to face a 25-month dispute over duplicate records.
An accountant who confirmed PAYE records were accurate, only for HMRC to move payments to the wrong tax periods — leading to debt collection letters and YTD discrepancies for employees.
In many of these cases, even when employers could prove the issue was on HMRC’s side, the burden was still on them or the employee to resolve it - often through months of follow-up and unclear processes.
How you can support your clients
While these problems may feel out of your control, there are ways to be proactive and position yourself as a steady hand:
✅ Set expectations early – Make sure clients know that RTI errors are not always caused by their payroll provider. HMRC’s systems are not infallible.
✅ Push for transparency – Encourage clients to give you authorised access to speak with HMRC. Sometimes, the workaround is persistence.
✅ Work with a specialist payroll bureau – Partnering with a payroll provider that actively tracks RTI discrepancies, audits submissions, and supports you with dispute resolution can save everyone time.
✅ Document everything – Maintain a clear audit trail of submissions, confirmation receipts, and correspondence — especially if you need to push back against an incorrect charge.
The Recommendations
The CIPP has called for HMRC to:
Improve transparency and access to RTI data
Allow employers and agents to view HMRC’s RTI records
Staff helplines with people who can actually resolve issues
Review RTI’s current functionality before mandating further expansions (such as payrolling benefits)
These are changes we should all be championing — because the current system is creating unnecessary work, confusion, and cost for everyone involved.
Final thoughts
Whether you handle payroll in-house or refer it out, you need to know what’s happening behind the scenes with RTI. This report from the CIPP confirms what many of us have suspected for years - the system doesn’t always work the way it should.
But with the right awareness, partnerships, and persistence, you can help clients navigate the chaos with confidence.
📄 Source: Systemic Issues in HMRC RTI Data Collection, Chartered Institute of Payroll Professionals (2024)
Need support or just a chat through - Reach out to Austin on austin@yourpayrollmanager.co.uk
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