But Paul Gray, director general health and social care and chief executive of NHS Scotland, has been condemned for again leaving it to NHS Lothian to carry out the inquiries.
Dr Jane Hamilton has been appealing to the Scottish Government for years to seek an independent view of her concerns over the management of the Mother and Baby Unit at St John's Hospital, Livingston.
She has also made allegations of harassment, bullying and victimisation after she "blew the whistle" over the safety of the unit more than five years ago.
NHS Lothian insists all her concerns have been fully and independently investigated.
Scottish Health Secretary Alex Neil has so far accepted these assurances and been reassured by a report by the Royal College Of Psychiatry, which awarded the unit a rating of "excellence".
However, Dr Hamilton and others have challenged the independence, relevance and scope of these testimonials.
She has now lodged an official complaint against a senior health figure central to what she sees as a cover-up within the body. This relates to her serious clinical concerns, as well her own treatment by the health board.
A Scottish Government spokeswoman confirmed the complaint would be examined and defended the decision to pass it to the board.
She said: "A complaint was received by the Government relating specifically to the conduct of a member of staff in NHS Lothian. It is normal practice for an employer to be given an opportunity to investigate a complaint against one of its employees. It is therefore our intention to pass this to the board for investigation."
Tim Davison, chief executive of NHS Lothian, said: "I can confirm I have been asked by the Government to investigate a complaint about a member of staff and am setting up this investigation."
But Dr Hamilton, who has never been allowed to return to her specialist position in the Mother and Baby Unit, has already expressed serious reservations to NHS Scotland about an internal investigation, in which NHS Lothian will again scrutinise itself.
Neil Findlay, Scottish Labour's health spokesman, agreed, saying: "Dr Hamilton was brave enough to come forward about her concerns and she has been treated appallingly for doing so. I do not think it is right the same health board is allowed to investigate her complaint.
"There should be an independent investigation able to do that if somebody comes forward with significant issues. They should be looked into without that person fearing for their job."
He said NHS staff needed to know they would be listened to and need never feel intimidated about raising concerns about patient safety and any questionable practice in the NHS.
"There has to be a system in place that provides for that and allows staff to feel confident in raising issues," said Mr Findlay.
Dr Hamilton was an established consultant specialising in perinatal psychiatry who moved from England to take on this new post when the service opened in 2007. She was the only perinatal specialist there.
When she came to work in Scotland she had an unblemished and distinguished professional record and had been asked to co-author the National Institute For Health Care Excellence guidelines for clinical practice in her field.