Civil service union chiefs said on Friday they had requested the legal support for top officials who were forced to navigate a "complex minefield" which involved criminal and civil litigation.
Dave Penman, general secretary of the FDA union, said civil servants had been made "scapegoats" by committee members who chose to operate their hearings in quasi-judicial manner.
It emerged this week through a Freedom of Information request that £54,378 was spent on external assistance to help prepare six officials ahead of appearances before the committee.
It prompted criticism from opposition MSPs on the committee and claims that witnesses had been "coached”.
But Mr Penman said: “Once again civil servants find themselves as convenient scapegoats for the decisions of politicians.
"In what was already a complex legal minefield involving both criminal and civil litigation, the Committee on the Scottish Government Handling of Harassment Complaints chose to conduct its hearings in a quasi-judicial fashion, requiring witnesses to give evidence under oath.
“In those circumstances, and as would be standard practice, we pressed Scottish Government to ensure that civil servants were provided with legal support when considering their evidence.
"It is galling to now see committee members line up in the press to criticise the cost of this support when it was their decision in the first place that necessitated this expenditure.
"It is also frankly hypocritical when the committee itself has a lawyer attending hearings to advise on complex legal issues, including potential breaches of court orders."
The committee was established after the former first minister won a judicial review in January 2019 against the government he led for seven years over the way it handled harassment complaints against him made by two civil servants. Mr Salmond was separately cleared of a string of sexual assault charges at the High Court last year.
Tory committee member Murdo Fraser had described the legal support for witnesses as "coaching them in advance”.
The committee has complained about a lack of co-operation from the Scottish Government during its inquiry.