It follows allegations made during a BBC Scotland documentary the contract award process for hulls 801 and 802 for the Clyde and Hebrides was rigged in favour of Ferguson Marine, then owned by Scottish Government economic adviser and Yes-supporting businessman Jim McColl.
The shipyard also told the Scottish Parliament’s net zero and transport committee that hull 802 would be three months late, with the ferries likely now to cost three times more than their original budget.
That would mean a total cost of around £300 million, including some £83m previously spent, compared to the original contract of £97m.
Mr Ross challenged the First Minister on the fact Ferguson’s received a key document, what he labelled a “cheat sheet”, which was not shared with other competitors.
He said: “The only conclusion that any reasonable person could draw is the deal was rigged. But we didn’t find out any of that until this leaked dossier was uncovered by investigative journalists this week.
“Instead, we got secrecy. The public were kept in the dark. It’s clear that there has been a cover-up by the Government and its agencies.
“The First Minister thinks this is no big deal, but this does matter – because the price and the delays keep spiralling further.”
He added: “This looks like corporate fraud and there is a stench of political corruption, but nobody has been sacked. The Government says nobody is responsible and nobody is to blame.”
Ms Sturgeon said the criticism from Mr Ross was inconsistent with previous accusations the Government pushed CMAL to agree the contract with FMEL against its will.
She rejected the accusations the procurement process had been “rigged”, stating ministers were not involved, they were not aware of any impropriety, and their job was to save employment at the yards.
The SNP leader said: “I will never apologise for the actions this Government has taken to save the jobs of the people who work in Ferguson’s shipyard.”
She added: "For months now, Douglas Ross has appeared to have alleged in this chamber and elsewhere, wrongly I hasten to add, that Scottish ministers directed, forced CMAL against its will to award this contract to Ferguson’s shipyard.
"Today it appears to be the case that Douglas Ross is alleging that CMAL actually in some way collaborated with Ferguson’s to ensure that the contract went to that shipyard.
"Perhaps Douglas Ross needs to get a little bit of clarity about the allegations he is making.”
Speaking with journalists, the First Minister’s official spokesperson later said the Government had not “detected the stench of corruption” around the process.
He also said it should not be assumed the projected cost of the ferry contract, issued by Fergusons as an additional £84m, would be the final figure for the work.
Ministers were also unaware of the delay to hull 802, which will now not be delivered until 2024, until a day or two before it was announced.
This is despite months of updates from the yard stating the previous timetable was challenging.