Figures given to The Herald show at least 390 staff left their jobs under compromise agreements last year and were paid more than £12 million from NHS coffers.
These deals involve an employee agreeing not to pursue an employment-related claim, normally in exchange for a cash sum. The number of people leaving this way has risen steadily over the past five years. Many of those who depart sign clauses preventing them from criticising the organisation or speaking about their reasons for going.
Jackie Baillie, shadow health secretary with Scottish Labour, said: "I am concerned that gagging clauses are being used to prevent any discussion about why some of these staff are leaving and that it allows the NHS to move people who raise concerns about safety from their posts.
"The General Medical Council advises against them, the NHS in the rest of the UK states that they should be used as an exception and a Select Committee in the House of Commons says that they should be scrapped. Why they are being used on such a scale in the NHS in Scotland needs to be explained."
She added that the figures reinforced the need for an independent helpline for whistle-blowers.
In December, Health Secretary Nicola Sturgeon said NHS staff should feel free to report concerns about patient safety. It followed a poll that suggested more than one-third of Scottish nurses had been discouraged or told not to report concerns about problems such as patient safety.
She said: "I will not tolerate a situation where NHS staff are told not to report patient-safety concerns." Some health boards use compromise agreements for voluntary redundancies. Union officials believe they can be helpful for some individuals.
However, there are concerns that compromise agreements are being used to get around the Scottish Government's trumpeted no compulsory redundancies policy.
One union source said: "My health board is actively using compromise agreements to effectively make people redundant without paying contractual redundancy fees and without attracting the interest of the health department ... The information we have locally is the health department is aware of the practice."
Another said: "The biggest reason for [exit deals] is you need to re-align your workforce and you just cannot afford to have someone sitting on your books. We say we have no compulsory redundancies, but we do."
NHS Greater Glasgow and Clyde admitted under Freedom of Information legislation that last year 54 employees left the board with such deals "rather than be redeployed into a suitable vacancy as a result of service redesign". They were paid £1.9m and since April this year another 24 staff have signed similar deals.
Across Scotland, FOI responses from the health boards show at least 131 agreements were brokered in 2009-10; 217 in 2010-11; and 390 in 2011-12. Most health boards said the deals included "non-disclosure" clauses although some refused to provide this information. Two regional health boards have not answered the request.
Theresa Fyffe, director of the Royal College of Nursing Scotland, said: "We would be concerned if health boards were routinely using compromise agreements to get around the Scottish Government's 'no compulsory redundancies' pledge as they chip away at their wage bills to cut costs.
"We know that health boards have been saving money by simply, for example, downgrading staff or not replacing them when they leave, and this may be another way of hiding cuts to the nursing workforce."
Matt McLaughlin, Glasgow health organiser for Unison, said: "We support the Scottish Government's policy around no redundancies in the NHS. However, the detailed circumstances in Glasgow show that there is a disjoint between the policy and the application on the ground."
Patrick McGuire, partner at Thompsons Solicitors, said: "These NHS figures raise concerns about the conduct of the institution."
A Scottish Government spokesman said: "The health service workforce changes to match clinical need and the Scottish Government has a policy of no compulsory redundancies in the NHS.
"When organisational change occurs within NHS boards there may be staff who become displaced. These staff have the option of being redeployed into suitable alternative employment or, in some cases, they may opt for voluntary severance where this is available.
"Compromise agreements set out the terms of the package for both the employee and the employer who should both seek legal advice before proceeding."