Bonuses totalling £142,748 were paid to more than half of the staff at the Office of the Third Sector between 2007 and 2009.
The Cabinet Office, which houses the OTS, published the figure last week almost three months after Third Sector requested the data under the Freedom of Information Act.
Of 69 OTS staff in 2007/08, 41 received bonuses totalling £63,092, an average of nearly £1,539 each. Of 64 staff in 2008/09, 36 shared £79,656, an average of £2,213 each.
The Cabinet Office said: "These payments are used to drive high performance and form part of the pay award for members of staff who demonstrate exceptional performance, for example by exceeding targets set or meeting challenging objectives."
It said the payments were funded from existing budgets and would not add to future salary costs.
Third Sector submitted the request on 3 March. It referred the matter to the Information Commissioner's Office after no response was received within the required 20 working days.
In a decision notice published last week, the ICO ruled that the Cabinet Office had breached freedom of information laws.
Gerrard Tracey, principal policy adviser at the ICO, said: "The public authority did not deal with the request for information in accordance with the act."
A Cabinet Office spokesman apologised for the delay, saying it "reflected the heavy workload faced by the Cabinet Office at that busy time".