August 2025’s Employer Bulletin made reference to HMRC’s new online form for reporting a PAYE Disputed Charge. This has been available since 31 July 2025. From 31 August 2025 you will no longer be able to report an Employers PAYE dispute through HMRC’s helplines or webchat.
ICB has publicised this form, however, wants to devote this article to the topic, highlighting the essential parts of HMRC’s ‘Get help to correct an employer PAYE bill’ guidance.
Why Use the Service?
A Disputed Charge is, simply, where the employer disagrees with HMRC’s systems’ calculation of the amount they are due to pay over.
On a monthly basis, as detailed in HMRC’s Debt management and Banking (DMB) Manual, their Enterprise Tax Management Platform (ETMP) will look at the totals on all Full Payment Submissions (FPS) for a PAYE reference. They do this by looking at the monthly FPS year-to-date values for Income Tax, National Insurance Contributions (NICs), Student Loans etc, reducing this by the previous month’s totals. Comparing one month’s year-to-date totals against the previous month’s will give them the total that they believe is due.
From this, HMRC will reduce the liability by any values submitted on the Employer Payment Summary (EPS), for example, reclaims for Statutory Maternity Pay (SMP).
So, essentially, HMRC’s ETMP will look at this tax month’s FPS, reduce it by this month’s EPS to calculate a value due for payment.
Of course, there are many reasons why HMRC’s calculation may disagree with the employer’s calculation for the payroll system. For example, maybe the EPS has not been submitted on time but, commonly, HMRC’s IT systems feeding into ETMP have created a duplicate employment. So, there are many reasons why HMRC may calculate one amount but the employer believes another amount is due.
This is a Disputed Charge.
Who Can Use the Service?
It is important HMRC’s calculation and the employers are aligned for fear of late payment penalties and interest charges. So, where there is a disagreement about the liability, the following can use HMRC’s new online form:
- The employer of the PAYE scheme; or
- An authorised agent acting on behalf of the PAYE employer
Therefore, bookkeepers can use this service.
Before Using the Service
It is important to have all necessary information at hand before using the service. HMRC’s guidance says that, in the first instance, you will need the following:
- The PAYE reference number;
- The Accounts Office reference number;
- The Self-Assessment or Corporation Tax Unique Taxpayer Reference (UTR); and
- The number of employees (from the payroll)
Further, you will need the following FPS values from payroll software for the tax year:
- Income Tax;
- Employer National Insurance contributions;
- Employee National Insurance contributions;
- Student loan deductions; and
- Class 1A National Insurance contributions
The details should be as they appear on your payroll software, not from your HMRC business tax account. Because of the way that HMRC calculate the liability, ICB also recommends having your EPS values as well.
Note that if you have a Disputed Charge for more than one tax year, you will need to submit a separate request for each year.
How to Use the Service
The online form is available by signing in with your Government Gateway user ID and password.
After Using the Service
Once the query has been logged, HMRC will send a confirmation E-Mail with a unique refence number. ICB strongly recommends you keep note of this.
HMRC advise that they will make contact by telephone or email ‘within 40 working days to discuss your FPS information and help you to fix your payroll records’.
ICB notes that the inference is still that it is the employer’s fault and, maybe, there is an action that has created a duplicate employment that needs to be corrected. However, in this instance it is HMRC’s systems that need to be corrected.
Further, note that the charge is created by looking at both the FPS and EPS and discussing only FPS information may not be the resolution.
For Bookkeepers
ICB welcomes this service, however, advises members to have all information to hand before using it and when HMRC make contact. We agree that it could be an error in payroll systems and HMRC’s advice in this regard will be useful. However, the important things is that HMRC’s systems replicate the information in your payroll system if you know that this is correct. It could be, then, that it is HMRC’s systems that need to be corrected.
