Two senior council officers who were suspended on full pay are to receive almost £300,000 in pay-offs.
Caerphilly council's deputy chief executive Nigel Barnett and head of legal services Daniel Perkins were suspended in 2013 after a Wales Audit Office report on salary increases.
At a special council meeting on Tuesday, councillors decided that their employment would end immediately.
"It draws to a close a most difficult period," the council said afterwards.
The former chief executive Anthony O'Sullivan is also on "special leave".
Mr Barnett will receive £171,000 and Mr Perkins £127,000 as "compensation for the loss of their employment and on condition that this brings matters to a close".
In both cases, the council said the settlements were "considered to be much less than would have been the cost of continuing with a disciplinary investigation" which would have taken a further 12 months.
It was claimed in September 2012 that the three officers agreed to give themselves 20% pay rises when most council staff faced pay freezes.
The pay rises were later changed to smaller increases.
A police probe into the affair led to a criminal case which was dropped in 2015.
An internal investigation has been ongoing but councillors were asked to approve settlement deals for Mr Barnett and Mr Perkins on Tuesday.
Leader of the Plaid Cymru group on the council, Colin Mann, said many local people would be "naturally concerned and upset" that a financial settlement was being put forward.
Several councillors said there was broad support during the closed-doors meeting for amending the current legislation surrounding disciplinary matters to ensure similar delays do not happen again.
A statement released by the council after the meeting said there had been "considerable public interest in this uniquely difficult matter" and it wanted to make the settlements known in order to be "open and transparent".
The council said both Mr Barnett and Mr Perkins had "fully cooperated" during the investigation, and it reminded that criminal charges which had been "so heavily publicised" were dismissed.
"It would be wrong for any suspicion or stigma attached to that process to remain in anyone's mind," the council said.
The report considered by councillors contained no information on whether another settlement with Anthony O'Sullivan is likely in the near future.
Before the settlements were agreed, the overall cost to Caerphilly council was about £3m, with more than £2m paid in salaries to the three men over the period and £500,000 in legal costs for the council.