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HMRC internal manual

Debt Management and Banking Manual

Debt and return pursuit: PAYE RTI: disputes: disputed charge process

This process is for RTI disputed charges and does not cover:

  • specified charges
  • incorrect CIS charges
  • BROCS charges
  • interest charges
  • advances.

Existing dispute case

If there are IDMS/ETMP notes (the Charge Resolution Team (CRT) start their ETMP Dispute Review notes with RTI-PAYE-underpayment query) referring to an existing dispute case or the ETMP dispute flag has been set for the year queried by the customer, advise them:

  • we will not be able to give them a fix date as it depends on the issue involved with the charge
  • debt recovery action has been halted on the disputed element whilst we look into their case and they will be contacted in due course
  • the customer does not need to do anything (apart from continuing to pay any undisputed liabilities).

Do not make any new referral for this period (you can still make referrals for other periods that have not been sent). Do not attempt to chase the CRT.

If IDMS/ETMP notes indicate a dispute but the Disputed Charge flag is not set the dispute should have been resolved.

Check ETMP notes to see why the dispute has been resolved and pass that information to the customer (the CRT may also have passed information to the customer about which employee records need amending).

If the customer is still disputing the figure then follow the process below.

Establishing the charge

Where there is employer contact with DM and the employer does not agree with the amount of the charge, DM will use the following information to help resolve the issue and refer on as necessary.

Scenario Questions Action
Have all FPSs showing deductions been submitted? Has employer submitted all FPSs and received successful filing notification?  

What are the employer’s YTD figures?




Are there any indications that that additional works numbers have been created for individual employees in error? Compare with YTD figures on ETMP. If these don’t match, confirm the date the last FPS was submitted and if a successful filing notification was received.

Ensure employer submits further FPS or EYU as necessary.

If the YTD we hold doesn’t match the YTD the customer has then it will need to be fixed at the employee level. This means identifying which employees are incorrect and adjusting their record either on their next FPS or on an EYU.

If so, these are duplicate employments; refer case directly to PT Ops Charge Resolution Team.      
    When should corrections be done? They should be made on or before 19th of month.
If any corrections are made after the 19th, adjustments will be included in a later month and any unpaid amount from the earlier month should not be paid.    
  Have all payments been made? Has employer paid all payments due for the month?

Has employer checked all payments have been debited from their bank?

Has employer checked to see all their payments are shown on their Online Services account? Ensure employer makes any further payments necessary.


Carry out tracing actions if payment debited from bank and not on ETMP.      
    Are the payments in the correct place? Carry out reallocations as appropriate.
  Have all EPSs showing amounts to be recovered been submitted? Has the employer paid any recoverable statutory payments this tax year? If yes, has the EPS showing Year To Date (YTD) figures been submitted? When? Did they received successful filing notification? Ensure employer makes any further submission as necessary. Remember, any credit from an EPS will not be given until the end of the month in which it is submitted.
    What are the employer’s YTD figures? Compare with YTD figures on ETMP. If these don’t match, confirm the date the last EPS was submitted and if a successful filing notification was received.


Employer action required

Where it is established that the employer needs to submit additional returns which will correct the year-to-date figures, apply a suitable BF in IDMS.

Charge unresolved

If DM are unable to agree the value of the charge with the employer, refer the case on to the PT Operations Charge Resolution Team using the referral icon on your desktop, ensuring that you are set up as a ‘DMB User’.

DM will also:

  • advise the employer that as we are unable to reconcile the differences over the phone and we will refer their query to our dedicated Charge Resolution Team in the Employer Office who will review the position and get back to them
  • advise them that they may be contacted by this team and asked to submit further information in relation to the FPS submitted to date
  • ask the employer to pay the amount they calculate they are due to pay if they have not already done so and continue to pay any undisputed liabilities as they fall due
  • set the dispute flag on ETMP using the helpcard; for the current tax year on the current month, for the previous tax year disputes on month 12 or the last active month in that year
  • set a clerical interest lock on the charge in dispute if the amount is £9k or more and unpaid
  • generate a note on ETMP and IDMS that a disputed charge stencil has been sent and when this was done and including the year-to-date (YTD) figures up to the month under review, the month in dispute, the Full Payment Submission (FPS) amount, the Employer Payment Summary (EPS) amount, the payments received and the discrepancy figure.


Once a referral has been sent, the work item on IDMS needs to be moved to C/W Distraint, set on a next action of N/A Review and moved to MU 308314 unless they are Large Business Unit (LBU) cases which should be transferred to MU397118. Then:

  • set the BF from one month from today for underpayments of £100,000 and above, complaints, band type 1, for large employers (segmentation 1/LBU)
  • set the BF from two months from today for all other cases.