Construction of two fish farm work boats and an oil industry barge, which began before the Scottish Government nationalised the Port Glasgow yard in 2019 to avert its closure, caused losses of £7.8m, its annual accounts have shown.
A source said it raised questions about state aid rules because the orders were private contracts.
Scottish Labour described the figures as “eye watering” and said they added to the “catastrophic ferry fiasco that rumbles on with no end in sight”.
The work boats, Helen Rice and Kallista Helen, were completed in 2020 for Inverlussa Marine Services in Mull.
The third vessel, an air cushion barge, was finished the same year for CMI Offshore for the Caspian Sea.
News of the losses comes on top of the yard’s work on Glen Sannox and an unnamed sister vessel being built for use by CalMac running four years late.
The former is now due to be completed by September and the latter by July next year.
The shipyard has said the dates could be affected by Covid-related staff absences, but said operations were currently “continuing at the expected level”.
The ferries are now estimated to cost up to nearly £197m compared to the £97m original contract.
Ferguson Marine (Port Glasgow), the name of the yard under state ownership, confirmed the losses on the other vessels were a result of cumulative revenue of £3.5m up to March 2021 being outweighed by cumulative costs of £11.3m, comprising £10.1m to March 2021 and a net trading loss of £1.2m in the year to March 2022.
Its spokesperson said: “The decision to complete the contracts was undertaken with suitable due diligence.
“The contracts were originally placed with Ferguson Marine Engineering Limited and the vessels were under construction when Ferguson Marine (Port Glasgow) took control of the yard.
“All three vessels went under the same programme of remedial work that the two dual-fuel ferries had to have completed.”
A Scottish Government spokesperson said: “All Scottish Government investment in private companies must follow the guidance contained within the Scottish public finance manual and be supported by an appropriate level of commercial advice and due diligence.”
However, Scottish Conservatives transport spokesperson Graham Simpson said: “There are big losses on just three vessels.
"The question for the Government is why these vessels were built at a loss.
"How was the cost of construction allowed to spiral so that they couldn’t even break even?
“We should also be told who has paid for the loss – no doubt it’s the taxpayers again.”
Colin Smyth, his Labour counterpart, said: “The chaos at the heart of Ferguson Marine continues.
"The losses on these vessels are eye watering, adding to the catastrophic ferry fiasco that rumbles on with no end in sight.
"The Scottish Government should have taken action when they were first made aware of problems at Ferguson and with the Government’s own flawed procurement processes years ago.
"But the failure of ministers to do so means it’s the Scottish taxpayer that is picking up the bill for this mess and the workforce who continue to face uncertainty.”