The accounts for 2011-12 showed that the total cost of exit packages was £38 million, despite concern about public service cuts.
At the top end of the scale, two officials were given a severance package of between £200,000 and £250,000 on their departure
In all, 965 civil servants successfully applied for a package last year. According to the accounts, 198 civil servants received between £50,000 and £100,000, including the two receiving over £200,000.
The remaining 694 members of staff received less than £50,000. The Scottish Government and quangos spent more than £4.9 billion on salaries and £594 million on pensions.
When it came to the retirement plans for Cabinet ministers, the accounts disclosed that the most senior SNP politicians have built up pensions worth £493,000 since they came to power five years ago.
In the past year, £165,000 has been paid into their retirement packages.
Those pension arrangements do not include those for Alex Salmond, who receives a special pension worth half his salary when he steps down.
The Labour MSP Rhoda Grant said: “These are truly staggering sums of money, and a waste of public money. It begs the question if this is the price of the SNP’s failed economic policy – where by sacking public sector workers it’s costing more money than it saves.
“This is a disgraceful waste of taxpayers’ money when you consider that for the same amount of money, the Scottish Government could have paid for three brand-new primary schools, or a community health centre or saved 1,200 jobs from the public sector.
“John Swinney has questions to answer on this as the buck ultimately stops with him.”
The Conservative finance spokesman Gavin Brown called for a review of pay-offs.
“People will be shocked and angry, especially given the current economic situation, that the Scottish Government is using nearly £40 million in this way,” Mr Brown said.
The accounts were published the week after finance secretary Mr Swinney published the Scottish Government’s budget.
He was criticised by his opponents for producing a “timid” budget that did not do enough to combat the recession.
A Scottish Government spokesperson said: “The costs of our voluntary exit scheme will be recouped in three years and will deliver recurring savings of £13 million a year, as part of action to significantly cut our central spending.
“Last year alone, we achieved savings of over £64 million in our central spend. The terms are set by the UK Government.”