Scottish Liberal Democrat leader Tavish Scott challenged Alex Salmond to crack down on bonuses to quangos.
Scottish Enterprise spent over £912,000 on bonuses in 2008/09.
The Scottish Government has spent three years reorganising the agency, including cutting its responsibilities in half, but still recruiting a Chief Executive on the same six figure salary as her predecessor.
Speaking at First Minister's Questions, Mr Scott challenged Alex Salmond about his Government's policy on bonuses.
Commenting, Mr Scott said:
"Our Freedom of Information response shows that Alex Salmond's economic quango paid out £912,000 in bonuses last year.
"It was his Government that agreed to pay Scottish Enterprise's new Chief Executive the same £200,000 salary as her predecessor, even though they had cut the quango in half. Scottish Enterprise bonuses sit in his in-tray. He is responsible for signing them off. He dodged my challenge to crack down on this year's payout.
"Unemployment in Scotland is continuing to rise, with the claimant count up 36,000. The economy is still in recession and there's a squeeze on public spending. It's against this background that the SNP Government thinks that it's still right and fair to spend almost a million pounds on quango bonuses."
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