Scotland's public spending watchdog has raised concern over £87,000 paid in bonuses to six senior managers at Ferguson shipyard.
The auditor general said it was "unacceptable" the money had not been cleared by the Scottish Government.
The BBC understands the money was paid under former turnaround director Tim Hair, who was brought in in 2019.
Current chief executive David Tydeman said the firm had introduced greater transparency over incentives.
In a report to MSPs on Tuesday, Auditor General Stephen Boyle said the bonus payments were approved by the remuneration committee and based on a paper from Mr Hair, who was appointed by the Scottish Government after it nationalised the yard.
The report said he was paid £1.8million during his time at the Inverclyde yard between August 2019 and February 2022.
Unacceptable
Mr Boyle said: "It is unacceptable that performance bonuses were awarded to senior managers at the shipyard, without proper governance for such payments. The Scottish Government needs to make sure its rules over pay are followed by this public body."
He also warned about uncertainty over the completion of two lifeline CalMac ferries, Glen Sannox and the unnamed vessel 802.
The ships are five years behind schedule and three times their original budget.
Mr Boyle said there were uncertainties over the final cost of the ferries, when they will be ready and whether the yard has a viable future.
The report said another £9.5million is potentially needed for their completion.
The ships are due to be finished in May of this year and March 2024.
Escalating cost
Mr Boyle added it was deeply concerning that the cost of the two ferries had continued to escalate while island communities remained "significantly impacted".
Mr Tydeman said the funding gap identified in the report was "largely to cover increased contingency expenditure".
He said: "I would stress that the construction costs to build both vessels are not a major contributing factor to this funding gap.”
Mr Tydeman said the firm had taken on board the watchdog's remarks.
He believed there was a strong future for the yard.
The Scottish Government said it was a concern that Ferguson’s did not get approval for bonuses, but the firm's new senior management team was committed to consulting with the government on the issue in future.
Strategic business plan
It said it expected Ferguson’s to provide a strategic business plan to ministers "in due course".
Scottish Conservative transport spokesperson Graham Simpson said the report was "utterly damning" and called for an independent inquiry into the ferry scandal.
He said: "The SNP-Green government needs to urgently spell out what the future holds for the yard and if they are going to remain competitive in any future procurement processes."
Neil Bibby, Scottish Labour's transport spokesperson, added that islanders, taxpayers and yard workers were being "failed at every turn" with no answer on what went wrong.
And Scottish Lib Dem economy spokesperson Willie Rennie called for an urgent statement from ministers to explain the saga.