Taoiseach Brian Cowen has denied that civil servants are getting bonuses despite salary top-ups to reward "exceptional merit".
The payments were made last year to select staff in the Department of Finance but officials insist the additional money was owed under a wage deal.
Fine Gael claimed Finance Minister Brian Lenihan had presided over a bonus culture in the public sector, highlighting a 200,000 euro payout to the former head of the National Treasury Management Agency (NTMA) Dr Michael Somers.
Fergus O'Dowd TD, who uncovered the payments, said: "Brian Lenihan drafted the most unfair Budget ever seen in Ireland. Yet he has presided over and tolerated a bonus culture within certain sections of the public sector.
"Fianna Fail and the Greens already have an enormous credibility problem. But their standing, and that of Brian Lenihan, has taken a further blow with these revelations."
The Department of Finance said 27 of its officials last year received a total of 55,670 euro for work classed as "exceptional merit". It said a 1% pay increase was agreed in 1994 and some departments incorporated the hike into annual salaries. But the Department opted to pay it to long serving officials in bonuses.
Mr Cowen challenged Fine Gael, insisting the payments were not the same as the controversial 40 million euro bonuses to Allied Irish Banks executives.
"It's not a bonus actually, it's part of the overall paybill," the Taoiseach told the Dail.
But figures released to Mr O'Dowd revealed bosses of semi-state companies netted huge bonuses in 2009, including 40,539 euro for Horse Racing Ireland chief Brian Kavanagh and 9,628 euro for Waterways Ireland head John Martin. Dr Somers took home an extra 200,000 euro.
Mr Cowen claimed the Government wants non commercial semi-state bonuses scrapped.