All but one of the 148 settlement agreements signed since 2011/12 contained confidentiality clauses and the vast majority of the 697 from the last five years probably did too, NHS Scotland chief executive Paul Gray said.
Confidentiality clauses appear to be almost automatic policy at NHS Scotland, he told Holyrood's Public Audit Committee.
Settlement agreements set out the terms of a termination of employment or a dispute resolution, and can include confidentiality agreements which make it illegal to reveal these terms or even that the confidentiality clause exists.
Health Secretary Alex Neil initially claimed that confidentiality clauses are "very often" requested by the staff themselves, before relegating this to "sometimes" and then conceding that he has no supporting statistics but that he was "going by anecdotal evidence".
He will endeavour to provide data on the number of staff who have asked for confidentiality agreements "provided it's not in breach of a confidentiality agreement", he said.
He is reviewing confidentiality clauses in NHS Scotland to ensure they do not "hide what should be transparent", he said.
It comes amid concerns that "gagging clauses" were used to suppress problems in English health boards following a public inquiry into serious failings at Mid-Staffordshire NHS Foundation Trust.
Labour MSP Ken Macintosh said: "Do you think if 147 out of 148 contained confidentiality clauses that this is almost a matter of automatic policy?"
Mr Gray said: "It appears to be so."
Mr Macintosh added: "Do you think that maybe the vast majority of the 697 settlement agreements over the last five years contained confidentiality clauses too?"
Mr Gray said: "I would be speculating but it's probable."
Mr Neil said it is important to distinguish between "confidentiality agreements" and "gagging clauses", insisting NHS Scotland has a "robust" policy on whistleblowing.
"We have got the whistleblowing line, and ironically we get more calls from the rest of the UK than we do from Scotland although we can't do anything about them," he said.
"People who see anything in the NHS going wrong or some practice applied that should not be, I want them to blow the whistle.
"Gagging clauses are illegal and we don't do gagging clauses.
"We still have confidentiality agreements, very often at the request of the person who is signing the agreement with us because they may have their own medical information as part of that agreement or something within that that they do not wish to become public knowledge."
Mr Macintosh said: "Going back to the Cabinet Secretary's statement that 'very often these are inserted at the request of the individuals', can you give me any examples?"
Mr Neil said: "I said they are sometimes inserted."
Mr Macintosh said: "No, you said 'very often'. How many examples do you think you will be able to find of individuals requesting this given that they are automatically inserted into every agreement?"
Mr Neil said: "I think it would be very difficult to get a precise figure, but we will look and see if we can give some indication to the committee of the number of requests we get from people."
Mr Macintosh said: "Why did you say they are 'very often inserted at the request of the individual concerned' if you can't back it up with any evidence?"
Mr Neil said: "Well I'm just going by the anecdotal evidence I've collected in 18 months in this job."
Mr Macintosh said: "So we've gone from 'very often inserted at individuals' request', to 'sometimes anecdotally you understand'?"
Mr Neil said: "What I am saying is that confidentiality agreements should not be abused. We cannot legally include gagging orders.
"When people are leaving the NHS under difficult circumstances then the history going back over many previous administrations is that confidentiality agreements are drawn up.
"Sometimes some of the information the individual doesn't want to have released, apparently.
"But obviously there has been no statistical collection to date of that kind of level of detail. We will establish whether we can quantify that.
"Over the last three years we have signed 148 confidentiality agreements, but I don't have to hand exact numbers where employees asked for a confidentiality agreement.
"I'm happy to provide that - provided it's not in breach of a confidentiality agreement."
He added: "One of the reasons I am reviewing confidentiality clauses is because I want to ensure that they are not being used to hide what should be transparent.
"We have responded not just to Mid-Staffordshire but to the subsequent inquiries."