While the amount an employer is asked to pay by HMRC will normally agree to the Full Payment Submissions,  Employer Payment Summaries and underlying payroll records, there can be cases where there is a discrepancy. 

In the past, employers might have telephoned the Employer Helpline or used the HMRC webchat to find a resolution to such discrepancies. However, from  31 August 2025, these contact options are no longer available for PAYE disputes. Instead, employers must use HMRC’s new online service for PAYE disputed charges.  

The new service allows employers to get help with finding and correcting the error, and can be used either by the employer or by an agent acting on their behalf.

HMRC still recommend that employers check their submissions and consult with online guidance in the first instance. But where that does not resolve a discrepancy, requests should be made under the new service and will result in HMRC contacting the employer or agent within 40 working days to discuss what has been submitted and provide assistance with fixing the payroll records as needed.

If you believe that a discrepancy has been caused by a criminal attack, you should instead follow HMRC’s separate advice and notify HMRC’s fraud team.

This article reflects the position at the date of publication. If you are reading this at a later date you are advised to check that that position has not changed in the time since. 

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