Employer PAYE liabilities and payments – how are HMRC’s systems working?

As PAYE RTI nears the end of its second year, are HMRC’s debt management and banking processes working as they should? 

The Tax Faculty is keen to hear your feedback, good or bad, plus examples of any problems which we can raise with HMRC. We’d like to hear from you whether you are an employer or payroll agent/bureau or an adviser.

For example: 

  1. Is HMRC’s business tax dashboard showing correct figures?
  2. Are you being chased by HMRC for underpayments that are not due?
  3. Have wrong apparent underpayments that you have referred via HMRC’s employer helpline to their Disputed Charges Team (DCT) been sorted out? How long is it taking for the DCT to sort out mistakes?
  4. Has HMRC reallocated amounts on your employer PAYE account for no obvious reason and/or without telling you?
  5. Have specified payments been added to your employer PAYE account when they should not have been, and which cannot be deleted?
  6. Are you having problems with obtaining repayment of overpayments, including accidental overpayments, for example, payments made twice or the wrong amount paid?
  7. Are there still unresolved issues, such as wrong apparent underpayments and unexplained reallocations, outstanding from 2013/14 and earlier years?

Please let us know of any difficulties you are encountering in this area by posting a short comment below. If it’s easier, just indicate which numbered bullets apply to you.

We​​ would also like to hear about the process for submitting RTI returns – you can post comments on our separate forum post How well are the RTI processes working now?


  • I have just put the phone down to HMRC. Client P35 shows PAYE over payment of £2,500. We claimed in writing on 21 April as requested. Today informed letter was opened on 01 June and the date by which HMRC expects to deal with this and refund the client is November 2015.
  • I am still trying to deal with a pre RTI repayment of PAYE (2012/13) where a refund of PAYE to an employee in the closing months of a business exceeded the payable liability for the period. HMRC initially refused to make repayment without an "explanation being given" and until "RTI submissions were brought up to date". Well, the PAYE scheme was closed at the end of 2012/13 prior to the client being 'mandated into RTI', so that didn't apply". This was 27 weeks after the claim had been submitted. When HMRC replied to our response (a further 27 week delay) it was simply a re-iterated request fro information on the original claim. So 54 weeks elapse and no progress whatsoever. A formal complaint submitted a month ago has yet to be acknowledged, let alone resolved and the lack of urgency on HMRC's part means the company has to keep its bank account open to receive the £600 or so that is due (for which a bank charge of £5 is accruing each month) and then it will be struck off. Anyone would think it was their money - they don't seem to believe anything I or the client tells them as to how the overpayment arose and until they are satisfied the repayment will not be made. Imagine if the client owed HMRC £600 and was taking 27 weeks to reply to letters - bailiffs would have been instructed and assets seized by now. My client has seriously contemplated instructing County Court recovery proceedings.  
  • Barry - I had a similar issue with one of my clients and managed to get it resolved by using my Agent Account Manager and what now seemed to be called Agents' Issues Resolution Service (see www.gov.uk/agent-account-managers-in-hmrc)  It still took about 6 weeks but I did get resolution and a repayment for my client. Have you tried this yet?  Could be worth a go?
  • Re Item 5 specified charges, and item 2 HMRC debt collector chasing for underpayments which don't exist:

    We have had 4-5 clients who have received specified charges despite having already submitted a final EPS/FPS through our RTI compliant IRIS software. Moreover some of the companies have already been dissolved. Despite both above points, the clients are being seriously hassled by debt collection (first letter date 27 April not received until several days later - debt collector arrived at the door today).

    HMRC's systems seem unable to link up quickly enough or at all and HMRC's Employer's Helpline were"unable to see the already submitted final EPS/FPS".

    As agent we seem to be in a piral of incompetence caused by HMRC's inadequate IT systems, procedures and training.
  • So long as the rules mentioned here www.gov.uk/paye-for-employers apply, you wouldn't have to register. But there are other constraints besides salary (for example, if the employees have another job besides their work for you then you would have to register) so do check that link out.