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HMRC internal manual

Self Assessment Manual

Repayments: issue repayment: non-automatic repayments

Repayments made from SA
Uncleared payments
Repayment to card
Repayment by BACS or Payable Order
Repayment by CHAPS or Local Office Payable Order
Repayments made through OAS
Repayment authorisation (or cancellation)
PAYE/CODA repayment systems
Repayment issued to incorrect customer

Repayments made from SA

When a repayment is claimed SA function ISSUE REPAYMENT FROM OVERPAID BALANCE will be used to repay all or part of the credit balance direct from the SA system. This function is accessed from function VIEW STATEMENT and will be used where

  • Repayment is to made from a trust record or arises from an amended return
  • Automatic issue is inhibited and following enquiries it is agreed that repayment can proceed
  • A repayment is requested other than by the return and a credit balance is held on the SA record (see Note 1. below)
  • Following approval an SA repayment that has previously been cancelled using function VIEW REPAYMENT is to be re-issued

If a customer, or their agent, requests a repayment and daily penalties are accruing, you can issue the repayment clerically using function ‘ISSUE REPAYMENT FROM OVERPAID BALANCE’. When the function is accessed a warning message is displayed saying ‘Daily penalties are accruing’.

If the request is made by telephone, advise the caller that daily penalties are accruing for which a penalty charge will be created. Ask them to submit the outstanding return and before repaying, ask if they want us to retain part, or all, of the overpayment on the statement to cover the future penalty charge.

If the request is made in writing, you can ignore the warning message and make the repayment.


1. Where there are charges becoming due within the next 45 days, the amount available for repayment will be the balance remaining after these charges have been cleared. But if the customer subsequently requests repayment of the amount set against these charges, if the request is made before their due date, then a further repayment can be made
2. Where a clerical repayment is to be created in an amount of £250,000 or over, a form R49 must be completed and signed by an officer of grade 6 or an officer of grade 7 with the appropriate knowledge. The repayment can be created following the authorisation on the form R49, which should be retained with the latest SA return to which the repayment relates or customer’s file as appropriate


  • A repayment for the specified amount will be created
  • Repayment supplement will be calculated, if applicable
  • Details of the repayment (including the name and address of the repayment recipient) will be recorded and available for viewing at a later date

If the amount of the repayment exceeds £150,000 (excluding RPS), the method of repayment should be either BACS or CHAPS and, where possible, BACS should be the preferred option over CHAPS.

If these repayment methods are not appropriate and the customer insists on a Payable order, divide the repayment and issue two payable orders. See SAM110142 for further information.

Repayments greater than £250,000, irrespective of their method of repayment, undergo more robust security checks (R49 checks) so a payable order should not be split if the repayment is for more than £250k. Alternatively, follow the guidance at SAM110142 for Local Office Payable orders.

Uncleared payments

To minimise premature repayment there is a period of inhibition from receipt of a payment before it can be repaid. This period of inhibition is covered automatically for repayments processed from a return, but it is not covered automatically if the function ISSUE REPAYMENT FROM OVERPAID BALANCE is used.

When the function ISSUE REPAYMENT FROM OVERPAID BALANCE is used, a warning message will appear to draw the operators attention to the fact that a payment included in the credit balance due to be repaid has been received within the inhibition period. The inhibition period is 14 days from the date the payment is received and includes payments made by cash, giro and electronic means, that is BACS and CHAPS.

In cases where the warning message appears, the operator must not override the warning message to issue the repayment but should review the dates of the payments on the statement and B/F the case until the inhibition period has expired, at which time the repayment can then be issued.

Where a payment has been transferred in from OAS, the inhibition period will have already passed and the repayment can be issued immediately.

Repayment to card

The option to repay to card will only appear as an option where the system determines that certain criteria are met. For further information, see subject ‘Repay to card’ (SAM110116).

Where that happens you should select ‘card’ unless you have a good reason to select an alternative method. For example, there is a valid Deed of Assignment in place or the customer is bankrupt.

Repayment by BACS or Payable Order

Where a non-automatic BACS or Payable Order repayment is created on-line, the status of that repayment will be immediately shown as Draft.

The repayment may then be selected by the SA system for manual authorisation, at which stage the status will be updated from Draft to Selected. The repayment will then appear as a work item on the W028 Repayments to be Authorised or Cancelled work list (SAM71106) for authorisation or cancellation.

When the manual authorisation is completed the status of the item will be updated to Authorised or Cancelled Selected as appropriate. If not selected for manual authorisation, the status of the repayment will automatically be updated to Authorised.

Once the status is updated to Authorised the repayment details are forwarded automatically from the customer’s record to the SA Repayment System to issue the repayment and the status at this stage will be updated to Transmitted.

Note: When the status is shown as Transmitted the repayment will have been authorised within the last 2 days, but not yet issued. A repayment cannot be cancelled whilst the status is Transmitted.

When received by the SA Repayment System, the status of the repayment will be updated to Issued. The SA Repayment system will issue the repayment to the customer within 3 days of the date the repayment is authorised.

The customer should receive the repayment within 5 days of it being authorised, but this may be slightly longer for BACS repayments due to the processing undertaken by the bank / building society in order for the repayment to reach the customer’s account. If the status is shown as Rejected, this indicates that it is a BACS repayment that has been rejected by the BACS system. For more information see subject ‘BACS Repayment Rejection’ (SAM110030).

A repayment with the status of Draft, Selected, Authorised or Issued can be cancelled at any one of these stages and if cancelled, the status will be updated to one of the following

  • Cancelled Draft (repayment cancelled at the Draft stage)
  • Cancelled Selected (repayment cancelled following clerical review but prior to authorisation)
  • Cancelled Authorised (repayment cancelled after authorisation but before issue)
  • Cancelled Issued (repayment cancelled after issue following instructions from HMRC Finance)

This process also applies to automatic repayments processed directly from the return.

Repayment by CHAPS or Local Office Payable Order

If the repayment method used is CHAPS or Local Office Payable Order, the repayment will be recorded immediately on the SA record but will not be issued by the SA Repayments System. This must be done manually and the procedures to be followed are detailed in the Action Guide (SAM110142).

Although the VIEW REPAYMENT screen shows that a repayment notification has been issued for a CHAPS or Local Office Payable Order, this will not have been issued automatically by the SA system. Any repayment notifications for these type of repayments must be issued manually.

These type of repayments will not be selected for manual authorisation and following creation will have an immediate status of Authorised.


1. If the Welsh language signal is set the repayment method can only be by BACS or Local Office Payable Order. In both cases, send a completed R23 together with signed authority (and any other additional papers/instructions) to

HMRC Welsh Customer Service
HM Revenue & Customs
Thedford House
High Street
LL49 9BF | || | 2. | If your office does not have access to function ISSUE REPAYMENT FROM OVERPAID BALANCE, repayment must be made through OAS |

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Repayments made through OAS

The facility to repay through OAS will still be available where the issue of a repayment from the SA repayment system is not appropriate. This could arise, for example as a result of a repayment claimed in respect of a payment made in error. That is where a payment made to HMRC, is intended to satisfy a non-HMRC liability. Repayment in these circumstances may create a debit balance or a reduced credit balance on the customer’s SA record.

Where a repayment request is received by the

  • Banking Operations office
  • Local Office responsible for processing work

Or in some cases

  • Recovery Office

The office dealing with the repayment request will need to consider when preparing the SA331 OAS Allocation Form (available for completion and printing from SEES) for repayment, any SA charges becoming due within 45 days. In these circumstances the customer / agent should be advised that the overpaid amount will be allocated to the charge becoming due. If the due date of the charge is imminent you may wish to

  • Telephone the customer / agent and
  • Explain that by the time any payable order is received the charge will be due for payment

Note: Where the request is pursued, the customer is entitled to repayment until the due date of the charge is reached.

In addition, a check will have to be made by the office dealing with the repayment request to ensure that the amount being repaid does not relate to an uncleared payment.

Function TRANSFER FROM TAXPAYER CREDIT should then be used to transfer the payment(s)/ credit(s) from SA to OAS and is accessed from function VIEW STATEMENT.

A SA331 OAS Allocation Form should be completed and printed from SEES for each individual customer showing every transfer and should be authorised by the office dealing with the repayment request in order to provide the Banking Operations operator with the appropriate authorisation and disposal instructions.

Note: Take great care before using function TRANSFER FROM TAXPAYER CREDIT because it may trigger a reallocation and cause interest and / or repayment supplement to be calculated.

Repayment authorisation (or cancellation)

Repayments produced using SA function ISSUE REPAYMENT FROM OVERPAID BALANCE with a repayment method of

  • Card, BACS or Payable Order will be subject to the same security checks as those created from a return
  • CHAPS or Local Office Payable Order will be created with a status of authorised and will be subject to existing clerical and supervisory procedures

Repayments made using OAS will be subject to existing clerical and supervisory procedures within each Banking Operations office.

PAYE/CODA repayment systems

The PAYE/CODA repayment systems will continue to be used where the SA or OAS repayment system is not appropriate. This will occur where, for instance

  • An unemployment repayment is to be made through PAYE
  • A PAYE cessation repayment is claimed prior to transfer into SA (Note: For customers already in SA, PAYE cessation repayments should be made by the creation of a freestanding credit and repaid through the SA record)
  • The set-off of CIS deductions is to be made to an earlier year’s CODA liability. (Note: This will only apply to in-year repayment requests and is not appropriate where an overpayment arises from the SA return)

Repayments made outside of SA will be subject to existing clerical and supervisory procedures.

Where repayment or set-off has been made using the PAYE/CODA repayment system

  • Use SA function AMEND TAXPAYER SIGNALS to set the No Repayment signal. (The setting of this signal will prevent an automatic repayment and possible over-repayment being made when the return is received)
  • Use SA function MAINTAIN SA NOTES to enter a brief note recording the fact that a repayment / set-off has been made

Repayment issued to incorrect customer

(This content has been withheld because of exemptions in the Freedom of Information Act 2000)

(This content has been withheld because of exemptions in the Freedom of Information Act 2000)

(This content has been withheld because of exemptions in the Freedom of Information Act 2000) (This content has been withheld because of exemptions in the Freedom of Information Act 2000)

(This content has been withheld because of exemptions in the Freedom of Information Act 2000)