A leaked dossier suggests the process of awarding a £97m Scottish ferries contract may have been rigged.
A new BBC Disclosure programme - due to be broadcast this evening - indicates that Ferguson Marine Engineering recieved preferential treatment.
The two ferries are still being built for CalMac, but will be at least £150m over budget and five years late.
Deputy First Minister John Swinney said he was concerned by the findings and would look into the matter further, while Caledonian Maritime Assets Limited (CMAL) - which owns the ferries, ports, harbours and infrastructure on behalf of the government - defended the procurement and said an audit in 2018 found "no adverse issues".
The BBC documentary, however, states that CMAL may have broken its own rules by allowing Ferguson to go ahead with its bid, despite being unable to provide evidence of a builders refund guarantee.
Ferguson obtained a document from a design consultant setting out CalMac's technical requirements, while other bidders had to rely on a more limited specification.
The shipyard was also allowed to change its design halfway through the tender by developing a variant which was mentioned, but discounted, in its original submission. This change also allowed it to reduce its price by nearly £10m, making it more competitive.
CMAL assessors also held a "confidential", in-person meeting with Ferguson - the only bidder to receive one.
The Port Glasgow shipyard went into administration in August 2014, but was bought a week before the independence referendum by businessman Jim McColl.
A year later, his new firm Ferguson Marine Engineering, won the contract to build two dual fuel vessels for CalMac.
But by 2019, the business fell into administration again and had to be nationalised.
McColl told the Disclosure programme that he first looked into buying Ferguson at least two months before it went bust, but felt there were too many issues that needed "tidying up".
When he later agreed to buy the yard, he said there were "no sweeteners" - but that he insisted on a letter from Alex Salmond promising a £12m order for a small CalMac ferry to enable him to re-employ workers.
He said he had no knowledge of being given special treatment for the larger ferries, but accepted that having CalMac's requirements document was an advantage.
"With hindsight, it put us in a very strong position, because we were responding to what CalMac were looking for, and not what CMAL had put out to... the other yards," he stated, adding: "We didn't know about that at the time."
CMAL previously said that Ferguson was its preferred bidder due to offering the most detailed concept design, even though it was the most expensive.
However, a report from CalMac found that a rival bid from a Polish shipyard best met requirements, while an independent naval architect noted that FMEL's initial design was less efficient than others.
John Kerr, a former CalMac technical director who was asked to review some of the leaked documents, was surprised Ferguson was then allowed to submit a revised, far lighter design after the tender deadline, describing it as effectively "a new bid".
A procurement law expert told the BBC that claims of unequal treatment of bidders in tender processes can lead to breaches in EU law and potential legal action from unsuccessful bidders.
Edward Mountain, who was convener of a Holyrood committee that looked into the ferries scandal two years ago, told the programme he had "real concerns" that MSPs "haven't been told the whole truth about what happened in this procurement process".
Swinney responded: "It is material that I take seriously, about which I have concerns, which raises fundamental issues for me about the fairness and the appropriateness of the tender process."
However, he added that he was not aware of any interference by ministers or civil servants in the procurement process.
CMAL stated that new information contained in the programme would need to be "carefully investigated".
Following the 2019 nationalisation, the government appointed turnaround director Tim Hair, who reported it would cost an extra £110m to finish the vessels.
His 454-day tenure in the role cost the taxpayer almost £1.3m, but the BBC found that many at the company raised concerns about the number of managers being taken on, with little evidence of progress.
GMB convener John McMunagle said the concerns were raised at board meetings, where they highlighted that there were "managers everywhere" - but they could not get steelworkers.
The documentary revealed that last November, unions told Finance Secretary Kate Forbes they had lost confidence in the senior management team.
The following month, Hair announced his resignation.
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