A total of 697 such documents were signed in the past five years and accountability campaigners welcomed the move by ministers as helping to remove the culture of fear surrounding them.
The move follows the furious row over gagging clauses in severance agreements between health boards and workers about to leave employment, often after a dispute. Health boards have denied misusing the agreements.
The issue came to a head earlier this year when The Herald revealed that a whistleblowing doctor, Dr Jane Hamilton, was risking a six-figure settlement and possibly the sack by speaking of her refusal to accept a confidentiality clause.
Health Secretary Alex Neil had previously warned health boards against such gags and in February declared he was removing confidentiality clauses from settlements with NHS staff.
He said there was a perception they "could be used to prevent staff from speaking out about failures in care offered to patients".
But The Herald has learned he has gone further and has ordered that all compromise agreements be subject to government scrutiny.
Rab Wilson, the psychiatric nurse turned whistleblower who exposed failures in NHS Ayrshire and Arran, welcomed the news.
He said: "For far too long health boards have been acting like feudal barons; beyond the pale and accountable to no-one.
"I had a confidentiality clause arbitrarily slapped on me by NHS Ayrshire and Arran when there was no need whatsoever to do so - it was a crude attempt to effectively gag me, and my union, Unison, played along with it."
Dr Hamilton, a nationally recognised psychiatric specialist, had raised concerns about the mother and baby unit (MBU) at St John's Hospital, Livingston, and warned in writing that somebody could die.
Two mothers subsequently took their lives and the family of one is suing the health board.
Dr Hamilton had raised these concerns as "protected disclosures" which were supposed to come with safeguards for whistleblowers against victimisation. However, in the compromise agreement offered to her by NHS Lothian, they were classed as "grievances" and included in a confidentiality clause. It would have meant she could never publicly mention them again.
Her legal advice was that she was effectively being gagged. NHS Lothian consistently denied this, but subsequently removed the clause.
Police are investigating the case of Dr Hamilton after it was reported by Mr Wilson. It is a crime to prevent staff from raising concerns about patient safety or malpractice.
Dr Hamilton said yesterday she welcomed this further tightening-up and scrutiny of the use of compromise agreements "which have up to now clearly been frequently used to buy off and silence staff".
She campaigns in Scotland on behalf of Patients First, the body set up by the whistleblower Dr Kim Holt, who was victimised but ultimately vindicated in 2007 in the Baby P scandal in London.
It is calling for a fully independent watchdog with investigatory and disciplinary powers to protect and encourage staff and ensure quality care for patients.
A Scottish Government spokesman said: "We are putting in place new arrangements for the notification and approval of settlement agreements in the current financial year.
"We are currently considering consultation responses and will set out the new process in due course."