First Minister Nicola Sturgeon has told MSPs she is "absolutely horrified" by a photo of a woman allegedly taped to a chair and gagged by male colleagues.
Ms Sturgeon said she had asked a top civil servant to conduct a full review into the circumstances and report to her personally as soon as possible.
She claims it took place amid years of bullying and harassment at Marine Scotland's Scrabster office.
Ms Fitzpatrick, a Canadian national, said the incident happened in 2010 as a result of her blowing the whistle on a threatening and misogynistic culture at the Scottish government department's base on the far north Caithness coast.
The fisheries officer has taken her case to an employment tribunal.
In evidence to the ongoing tribunal, she claimed that one of the men involved, fellow fisheries officer Reid Anderson, told her: "This is what you get when you speak out against the boys."
Highlands and Islands MSP Rhoda Grant, who has been supporting 49-year-old Ms Fitzpatrick, asked Ms Sturgeon at First Minister's Questions whether she would now intervene in the case.
The first minister said she was limited in what she could say because of an ongoing tribunal and internal investigation.
However, she said: "I can tell the chamber I have this morning asked the permanent secretary of the Scottish government to conduct a full review of the circumstances of this case, a review of the actions already taken and a review of the actions proposed to be taken and to report to me personally on her conclusions as soon as possible."
The Scottish government is responsible for Marine Scotland, which is the watchdog for the fisheries and aquaculture industries in Scotland.
Ms Sturgeon said: "Bullying, abuse, sexism, racism, have no place in any work place and they will not be tolerated in the Scottish government or its agencies."
She added: "I an absolutely horrified at the photo.
"I am also horrified at the circumstances in which it is alleged to have been taken."
Ms Fitzpatrick has been off work sick since November 2016.
She claims that over a period of almost 10 years she was subjected to threatening and misogynistic behaviour.
The BBC has seen emails showing Ms Fitzpatrick tried to raise the alleged restraint attack with one of her managers soon after it happened but it appears to have not been taken seriously.
The manager said he would have "a word" with the men involved - Reid Anderson and Jody Paske.
He added: "I am sure they meant no harm and that was the boys just being boys."
Mr Anderson, who the BBC understands remains employed by Marine Scotland and has recently been promoted, did not respond to the allegations, although civil servants are usually unable to comment without government approval.
Mr Paske, who no longer works at Marine Scotland, told the BBC that the allegations were "lies".
He said: "These are false allegations. I can't remember the event you mention, but if it did happen, it would have been office banter. Just a craic. Certainly nothing to do with abuse."