A total of 90 deals were agreed during the 2024-25 financial year, up six on the previous year and the highest figure recorded since 2017-18.
It is also the second-highest total since annual reporting began.
The agreements cost a total of £3,267,520, including more than £2.13m in payments over and above what workers were contractually due.
That is slightly down on the previous year, when the cost was £3.9m.
The figures show the NHS accounted for the largest share of deals, signing 38 agreements during the year.
NHS Scotland accounted for 38 settlement agreements
The Scottish Government and its associated quangos accounted for 29 settlements, while Scotland’s colleges signed 23 agreements.
Confidentiality clauses were included in 28 of the deals.
Colleges accounted for more than half of those, with 15 gagging orders.
The Scottish Government and its wider public bodies used them in nine cases, while NHS Scotland used them in four.
The report states that ministers have a “general presumption against” using confidentiality clauses, and that they should only be included when both parties explicitly agree.
It also stressed that the gagging orders cannot be used to prevent individuals from raising concerns or making protected disclosures under whistleblowing laws.
The cost of the agreements varied widely.
The most expensive settlement recorded during the year was for a Scottish Government worker at £263,730.
Of that, £207,827 was salary and £55,303 was compensation.
The second largest was for NHS Scotland and was £121,736, with £120,736 in non-contractual costs and £1,000 in legal costs.
The third was again for the government and came in at £113,635. Of that, £53,614 was salary and £48,271 was compensation. The legal costs were £11,750.
The civil servant in that case signed a confidentiality clause.
Ten settlements exceeded the Scottish Government’s £95,000 cap on exit payments, with a combined value of just over £1.21m.
In each of those cases, ministers had to sign off the money.
Overall, Scottish Government departments and other public bodies recorded the largest total bill, spending £1,605,323 on 29 settlements. Of that, £991,314 was compensation.
NHS Scotland spent £886,140 across its 38 agreements, while the 23 deals in the college sector cost £776,057.
Settlement agreements are typically used to resolve employment disputes or bring a working relationship to an end without the need for tribunal proceedings.
The report states that agreements can only be considered where mediation or other processes have been exhausted and pursuing formal proceedings would involve “disruption to the effective and efficient operation of the service caused by an on-going dispute and the resultant stress on individuals.”
They can also be the used “to bring matters to a timely conclusion”.
It adds that organisations must ensure any settlement represents value for money, “Settlement agreements should only be used where they represent the most effective and economical way of resolving a dispute,” the report says.
While the number of agreements has increased, the Scottish Government said this should not automatically be interpreted as a negative trend.
In the report, officials argued the key issue is ensuring the agreements are “scrutinised effectively and that robust controls are in place” rather than trying to “reduce the number of cases”.
The report notes that the agreements represent a tiny fraction of the public sector workforce covered by the data — around 0.03% of total staff.
Craig Hoy, Scottish Tory shadow finance secretary, said: “These eye-watering figures are symptomatic of the SNP’s cavalier attitude to taxpayers’ money.
“Nationalist ministers should be reining in the payouts going to senior quango staff, especially at a time when they are hiking taxes and making cuts to public services.
“But the high number of confidentiality clauses accompanying these golden goodbyes suggests that the secretive SNP is more interested in saving itself criticism from departing staff than looking after the public purse.”
Dame Jackie Baillie said it was a significant amount of cash (Image: Newsquest)
Scottish Labour deputy leader Dame Jackie Baillie said: “This is a significant amount of money and Scottish taxpayers will be wondering whether it represents good value, particularly given the state of our public services.
“That many of them contain confidentiality clauses also demonstrates the SNP’s culture of secrecy, in which anyone who speaks out is punished.
“Scottish Labour is ready to offer people the chance to take a new direction, finally turning the page on 19 years of dismal SNP government.”
The Scottish Government was approached for comment.
