Dr Jane Hamilton warned the health board in writing that somebody could die in the mother-and-baby unit at St John's Hospital in Livingston. Two mothers let out of the unit later committed suicide.
Hamilton, who ran the unit, claims she was victimised after raising concerns, and refused to sign a severance agreement involving a six-figure settlement with NHS Lothian claiming it would gag her.
NHS Lothian insists it has not tried to gag the doctor and her right to be a whistleblower was specifically safeguarded.
The family of one of the mothers who committed suicide, Claire Donald, 37, is now suing NHS Lothian for medical negligence.
Her family back Hamilton, an experienced specialist perinatal psychiatrist, who has been suspended or off work with stress-related illness for four years.
First Minister Alex Salmond has defended the board, and said an independent investigation into the MBU had found no evidence to back Hamilton's allegations.
NHS Lothian medical director Dr David Farquharson said: "The confidentiality statement confirms that, for the avoidance of doubt, Dr Hamilton will not be prevented from making a 'protected disclosure'."
He added: "NHS Lothian has robust policies and procedures in place to ensure that staff feel able to raise any concerns and we actively encourage staff to highlight issues relating to patient safety."
But Hamilton said her lawyers advised her the health board's calling her clinical concerns employment grievances, which had to be withdrawn, was gagging.
She added: "The draft agreement would also have extended to my husband who is himself a senior consultant. He feels pretty aggrieved about that."
Rab Wilson, a former psychiatric nurse who uncovered errors surrounding 20 deaths in the NHS Ayrshire and Arran area, is outraged at what he sees as a clear bid to gag Hamilton, and has asked police to investigate.
Wilson won the Kay Carmichael Award for services to social justice. He said: "The Public Interest Disclosure Act makes such gagging illegal, when issues such as patient safety are involved."
He has seen the agreement Hamilton was asked to sign. He added: "They had classified specific clinical concerns about patient care and safety, raised on precise dates, as employment grievances.
"The deal was that she had to withdraw these so-called grievances and not mention them again, thereby air-brushing from history Dr Hamilton's genuine concerns and complaints. A wee line elsewhere about protected disclosures doesn't change that."
He is now petitioning the Scottish Parliament to ban all confidentiality clauses from NHS settlements.
Dr Kim Holt is the paediatrician victimised after warning of serious failings at the Great Ormond Street clinic in London which sent Peter Connelly, Baby P, home two days before he died in 2007.
She founded the Patients First group to make the NHS more open and accountable.
This week, Holt wrote to Scottish Health Secretary Alex Neil, saying: "I urge you now to commission a fully independent and open inquiry into the treatment of staff raising concerns at NHS Lothian."
Neil said he had been "absolutely clear" with NHS boards that staff should not be gagged over concerns about patient safety.
He had written to all Boards to say confidentiality clauses must not suppress the reporting of concerns
Neil added: "NHS Lothian has stated publicly the contract referred to does not preclude any disclosure of concerns about practice. The Scottish Government will seek further reassurance on this."
Neil Findlay, Lothian MSP and Labour's spokesman on health, said: "NHS Lothian appear to have learned nothing about how to deal with employees. Last year's report into the bullying culture of senior management should have brought about change but now we see a doctor whose motivation is clearly the care and wellbeing of patients being treated as though she herself is on trial."