Dave Penman, the general secretary of the FDA, criticised the handling of the Salmond inquiry by MSPs and said civil servants had been treated with “almost open hostility".
He also accused inquiry members of making “derogatory comments” about civil servants and “deliberately misquoting” oral evidence.
Mr Penman’s comments come after it was reported the Scottish Government’s permanent secretary, Leslie Evans, is set to be "thrown under a bus” by SNP members of the committee.
Ms Evans is one of several civil servants who have come under serious scrutiny for their role in the development of the harassment complaints process and their handling of the complaints themselves.
The committee is examining the botched handling of harassment complaints against Mr Salmond by the Scottish Government, which led to a £500,000 legal bill after the Government conceded a judicial review challenge on the grounds of the process being “tainted by apparent bias”.
Mr Salmond was also acquitted of sexual offence charges in a trial last year.
Speaking to The Scotsman, Mr Penman said there was little surprise MSPs were being accused of having reached a conclusion on the matter before the inquiry had concluded its work.
He said: “From the outset, members of the Holyrood committee have operated with almost open hostility towards civil servants, including an initial attempt to seek evidence in a way that could have caused them to breach the Civil Service Code.
“They chose to operate in a quasi-judicial manner, requiring evidence under oath, yet the obligations this brings appear only to apply to witnesses and not to the committee itself.
"Committee members have made points or personal remarks during questioning, including deliberately misquoting a response on official record made by one witness when questioning another.
“They have been happy to make public comment, as well as retweeting press articles that make derogatory comments about civil servants and their evidence.
"Is it any wonder that this leads to a perception that some of the committee members reached a conclusion long before the process was concluded?
“It can come as no surprise, therefore, that their last desperate attempt to exaggerate their own importance has been to leak the conclusions that target individual civil servants, who they know are publicly unable to defend themselves.”
Responding, the Scottish Conservatives, who have two members on the committee in Margaret Mitchell and Murdo Fraser, said the inquiry had become “farcical” and Mr Penman was attempting “to distract” from the issues raised.
A spokesperson said: "Our committee members have acted with courtesy and professionalism as they attempt to find out why the female complainers were failed by the SNP Government.
"The committee's work has been routinely obstructed and numerous senior civil servants, including Scotland's most senior, have been required to correct their evidence.
"It has also emerged that around £75,000 of taxpayers' money has been spent preparing witnesses.
"The inquiry has become farcical and these gripes sound like an attempt to distract from these serious issues."
The other parties were also contacted for comment.