Sir Peter Housden, the permanent secretary to the Scottish Government, also said he had "concluded that we should strengthen the process" a number of public bodies must follow when agreeing such deals.
Compromise agreements - also known as settlement agreements - can see former employees receive cash payments in return for agreeing to make no further claims against an employer.
Earlier this year Hugh Henry, the convener of the Scottish Parliament's Public Audit Committee, said he was "extremely disappointed" with the response the committee had received from Sir Peter on the issue.
Sir Peter had told the committee then that the Government had "not at this time sought to collect central data" on the use of such deals in the public sector.
But in a letter he told MSPs: "I am sorry if I did not make myself sufficiently clear in our earlier correspondence."
Sir Peter had previously indicated the issue was being kept under review, and he went on to tell the committee: "I have now concluded that we should strengthen the process set out in the Scottish Public Finance Manual (SPFM)."
This will mean a number of bodies, including Scottish Government executive agencies, some tribunals, health boards and the Crown Office and Procurator Fiscal Service, will have to consult the Scottish Government when settlement agreements are being considered.
The Scottish Government would also have to be notified when such deals are finalised, and the organisations would also have to report on the use of settlement agreements, for example by including this in their annual reports.
Sir Peter said a consultation would take place with the organisations involved to "examine how we can best place data on settlement agreements in the public domain".
He added it was the intention that these new procedures would be adopted and in place in the financial year 2014-15.
In September Labour MSP Ken Macintosh, a member of the Public Audit Committee, said he had carried out research which showed 12,500 such agreements had been made across the public sector in the past six years, with payments totalling ''at least'' £52 million.
He told the committee at the time he had used Freedom of Information (FoI) laws to find out about the use of the agreements by public bodies.
Mr Macintosh said today the changes outlined by Sir Peter were a "clearly a huge step forward".
He said: "This is a very welcome letter and a very welcome change of tone from Sir Peter Housden. He starts off with an apology and I'm delighted that he has taken that note, rather than the previous rather abrupt, offhand and dismissive letter to the committee."