Former Welsh Secretary Alun Cairns received a “compensation payment” of £16,876 from the UK government last year.
A spokesman for the Vale of Glamorgan MP said the payment was “in common with the departure of every minister”.
Mr Cairns resigned in November over claims he knew about a former aide’s role in the collapse of a rape trial.
He insisted he did not know the details of the case.
An annual accounts report from the UK government’s Wales Office, published last month, says Mr Cairns’ ministerial salary for 2019-20 of £57,379 included the “compensation payment” of £16,876.
The full annual salary for this role, which he received in 2018-19, is £67,505. Government ministers are entitled to these salaries on top of their salaries as MPs.
From 1 April 2019, the basic annual salary for an MP is £79,468 plus expenses.
A spokesman for Mr Cairns said the compensation payment after his resignation was “in common with the departure of every minister from the Welsh or UK government and has been in place for decades, from Rhodri Morgan to Peter Hain”.
The Wales Office has been approached for comment.
Why did he resign?
In April 2018, Mr Cairns’ former aide, Ross England, made claims about a woman’s sexual history during the rape trial of his friend James Hackett, causing the case to collapse.
Hackett was subsequently convicted of rape at a retrial.
In December 2018, Mr England was then selected as the Vale of Glamorgan candidate for the 2021 Welsh Parliament elections.
At the time of his selection, Mr Cairns endorsed Mr England as a “friend and colleague” with whom “it will be a pleasure to campaign”.
The former Welsh Secretary denied knowing about Mr England’s role in the collapse of the case, but BBC Wales saw an email sent to him in August 2018 which mentioned the matter.
Mr England was suspended as a candidate and as an employee after details of the court case emerged, with the party saying a full investigation would be conducted.
A UK government Cabinet Office investigation was launched following Mr Cairns’ resignation from Boris Johnson’s cabinet in November.
Mr Cairns was cleared of breaking the ministerial code, but an inquiry found it “unlikely” he had not been made aware of Mr England’s role in the trial’s collapse.
The rape victim previously told BBC Wales that she was “disappointed but not surprised” by the investigation’s conclusion.