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HMRC internal manual

COTAX Manual

HM Revenue & Customs
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Repayments / reallocations: repayment / reallocation authorisation: R49 check for large repayments

Selection of cases

An R49 check must always be carried out whenever a repayment of £250,000 or more is generated either automatically or clerically by the responsible office. This includes cases where there is more than one repayment being made at the same time to the same company and the total being repaid equals or exceeds this amount.

The check should be carried out whenever the following occur or there is any other large CT repayment.

  • A large repayment is created on COTAX which will be sent out by automated Bacs.
  • A large repayment is created on COTAX which will be sent out by manual payable order.
  • A large repayment is created on COTAX which is reallocated into OAS for repayment by the CT unit at Cumbernauld.
  • A large repayment created by an amendment to a SAFE charge, including archived CTA charges.

Role of the R49 Checker

The role must be carried out by an officer of Grade 7 or above who is independent of the team generating the repayment and who has the appropriate technical knowledge, on the basis that they will be able to apply their skills and form an opinion on the accuracy and validity of the repayment. They are responsible for authorising the repayment as being accurate in all respects.

It is extremely important they carry out this role as it:

  • provides extra assurance on larger repayments
  • recognises there are additional risks to the exchequer and frequently detects human error.

If any business area wishes to amend the role of the R49 checker, they must submit proposals to CTIS for approval, using the CT Process Team, Mailbox (CTIS CT and Business Income Tax) email address. The proposals must include a risk assessment of incorrect repayments claims being made and governance processes to address the risk.

Checks to be made by the R49 checker

It is the responsibility of the caseworker to complete page 1 of the R49 and the following, all of which can be found on SEES. Where the repayment is to be made:

  • using OAS, a form CT251
  • from the SAFE system, a SAFE 1 (New) stencil
  • from a CTA archived charge, a SAFE (2) stencil
  • by manual payable order, a PORF.

The caseworker should pass these along with all relevant papers and the R49 (pages 1 and 2) to the R49 checker and use COTAX function NOTE to show ‘R49 raised’.


  1. Where the caseworker is below the grade of Band O they should arrange for the R49 to be checked by a Band O or above before it is passed to the R49 checker.
  2. Depending on local arrangements, the caseworker may save the R49 as a Word document and electronically submit the case to the R49 checker.

On receipt of the R49, the checker must review the repayment before completing page 2 of the form and where appropriate, complete the CT251 and SAFE stencil with their name and PID in the R49 box. They should use their knowledge and experience along with the questions on page 2 of the R49 to assist them. They should treat all repayments as potentially incorrect or suspicious.

Where the checker approves the repayment, the case must be passed to the Repayment Security Authoriser (RSA) to complete the R400 security checks except where the repayment is being made for a:

  • local compliance record and is being made through the OAS system
  • local compliance record and is being made from the SAFE system
  • LB record and is being made from the SAFE system for an amount less than £250,000.

In these cases the CT251 or SAFE stencil should be sent to the CT Unit in Cumbernauld or the Miscellaneous Charges unit in Shipley respectively, to carry out the security checks and make the repayment.

A paper or electronic copy of the R49 must always be kept in one of the following:

  • the file
  • shared workspace record
  • R49 batch.

Where the checker does not approve the repayment they will either return the case to the RSA or caseworker for the repayment to be cancelled.

It is the RSA’s responsibility to ensure they have been given an approved R49 before carrying out the R400 security checks and authorising the repayment. Once they have done this, they make a COTAX note ‘R49 authorised and filed at (the appropriate location)’ and retain the R49 in the establishment file.


  • COM120100 for guidance on completing form CT251
  • COM124051 for a list of forms relevant to this subject.