A total of 2.14million was given to officials during 2008-9 – a rise of 100,000, despite the recession and widespread public sector pay freezes.
The figures, disclosed in a parliamentary answer from finance secretary John Swinney, reveal that senior civil servants took home payments ranging from 7,000 to 15,000, with more junior staff given between 750 and 1,500.
Staff in the Scottish Government's change and corporate services department took home the most – pocketing 264,875 in payments. The legal services team shared a pot of 88,600, the police and community safety department were given 72,600 and HM Inspectorate of Education received 69,700.
Conservative MSP John Lamont, who obtained the information, said: "Many taxpayers will be astonished that the government is doling out bonuses of 15,000 to top civil servants."
The Scottish Government hit back, pointing out that senior officials are due to take a pay freeze this year.