Opposition politicians have called for an investigation into whether ministers broke the law and for “gagging orders” on former shipyard staff to be lifted.
Business minister Ivan McKee insisted the Scottish Government had been “absolutely transparent”.
It follows ongoing controversy over a botched contract to build two ferries at the Ferguson shipyard in Port Glasgow.
The vessels, the Glen Sannox and the as-yet-unnamed hull 802, are at least £150 million over budget and five years late.
A recent report from Audit Scotland found there was “insufficient documentary evidence” to explain why the contract was given to the Ferguson shipyard, which has since been nationalised, without a full refund guarantee.
Speaking in Holyrood, Labour MSP Daniel Johnson said: "Written authority from ministers should be required for this, yet no record can be obtained by Audit Scotland.
"The Auditor General described this as frustrating. He is being charitable.
"It is at best negligent and incompetent, at worst it could be unlawful."
He called on Mr McKee to commission an investigation into the matter "to establish the facts and, critically, whether or not the law has been broken".
Mr Johnson said there was a "pattern of opaque decision-making" by the Scottish Government.
He said: "The pattern is of due process that is deficient, lacking transparency and deliberately distorted to suit political ends rather than public interest.
"You could call this many things: negligent, incompetent, deficient.
"But when these decisions have all been wilful and deliberate, the word I would use is corrupt – perhaps not for individual gain, but corruption of the process for party political gains, contrary to the public interest."
Conservative MSP Graham Simpson said: "This is institutional corruption on a grand scale.
"Ivan McKee is showing breath-taking arrogance if he thinks there has been any transparency over this.
"This is the SNP's secret Scotland at its worst."
Mr McKee said the Scottish Government had been “absolutely transparent about the decision-making process and the information which informed those decisions”.
He said: "There's a clear audit trail of key decisions and the basis on which they were taken.
"In relation to the documents mentioned in the Audit Scotland report, a thorough search has been conducted and no ministerial response to the submission of October 8, 2015, has been located.
"As outlined in the Audit Scotland report, we have committed to a formal review following completion of the vessels project."
Mr McKee said Ferguson was still employing "hundreds and hundreds of people" and was "keeping commercial shipbuilding on the Clyde alive".
He said: "This Government makes no apology for being committed to supporting Scottish industry."
Elsewhere, he said the yard had announced the completion of a "major milestone" in the construction of hull 802, which has been fitted with its 100-tonne large bow unit.
Tory MSP Douglas Lumsden later asked if the Scottish Government would agree to lift "gagging orders" in place at the shipyard.
Auditor General Stephen Boyle previously said one individual was unable to give evidence due to a non-disclosure agreement (NDA).
Mr McKee did not directly address the question.
Last week, First Minister Nicola Sturgeon said it was “regrettable” that “a key point of decision-making” had not been recorded.