MSPs were told of “rumours” that top legal advisors to the Scottish Government had threatened to quit over the botched judicial review which was lost to the former First Minister.
Nicola Sturgeon was also forced to "recuse" herself from a recent meeting of her own cabinet when the Salmond Holyrood probe was raised, Deputy First Minister John Swinney told Parliament.
MSPs voted 65-55 in favour of a Tory motion calling for the publication of the legal advice which the Government received in relation to the judicial review brought by Alex Salmond two years ago. He launched the legal challenge over the Scottish Government's handling of complaints made against him by two civil servants. A similar vote in Holyrood was lost three weeks ago by ministers.
Tory MSP Murdo Fraser said the outcome was a "crushing blow" to Mr Swinney who is heading the Scottish Government's response to the Holyrood inquiry as a result of Nicola Sturgeon's involvement in the process.
“It’s clearer than ever that the SNP have something damning to hide," Mr Fraser added.
"They won’t release these key legal documents that would finally shed light on how complainers were failed and why more than £500,000 of taxpayers’ money was lost.
“The Parliament made clear today that there is nowhere to run or hide for the SNP. The Scottish Conservatives and every opposition party will continue to demand the release of these vital documents.”
The Scottish Government's case collapsed after it emerged that the investigating officer dealing with the complaints against Mr Salmond met with one of the complainers the day before she lodged the complaint. Mr Salmond was separately cleared of a string of sexual assault charges earlier this year.
Mr Swinney said that legal advice is generally not released in order to ensure that full and frank advice will be provided, without any concerns that it might be made public in future.
The Deputy First Minister said that over 1,000 pages of documents have already been provided to the committee - with at least a further 1,000 processed for release again.
But he added: "We need to take the necessary time to consider these issues and to formulate a proper response to the decision that Parliament took a few weeks ago."
But "no final decision" has been reached on the issue, he added.
"I confirm this issue was discussed with the cabinet yesterday," he added.
"The First Minister recused herself from that part of the meeting as is, of course, appropriate."
Labour MSP Jackie Baillie accused the Scottish Government of showing “utter contempt for Parliament.”
She added that the SNP had backed a Labour motion in the Commons demanding that the Brexit legal advice be revealed – which the UK Government did after losing a vote in Parliament.
She added: “Will the Deputy First Minister publish the legal advice – at the very least the written opinion from the senior counsel Roddy Dunlop QC.
"Rumours abound that senior counsel threatened to resign in the latter stages of the judicial review, so bad was the Scottish Government’s case and the determination of civil servants to plough on regardless.”