The vessels – the Glen Sannox and as-yet-unnamed 802 – are due to be delivered next year, five years later than planned and costing at least two-and-a-half times more than originally stated at around £250 million.
The ships are being built at the Ferguson Marine shipyard in Port Glasgow, which was saved by the Scottish Government from administration in 2019.
A report from Audit Scotland earlier this year found there had been concerns raised by ferry procurer Caledonian Maritime Assets Limited (CMAL) about the lack of a full refund guarantee from Ferguson Marine as part of the contract – which would act to shield public money if there were problems with the construction.
The report also found there was “insufficient documentary evidence” detailing why the contract was signed regardless.
One document, released by the Scottish Government last month, showed a previously unseen email trail where then-transport minister Derek Mackay approved the contract.
The document was given to the Scottish Government just hours before a debate on ferries called by the Scottish Conservatives.
But a senior Transport Scotland official has said there was nothing nefarious in the timing of the release, contrary to the accusations of opposition politicians.
Fran Pacitti, the director of aviation, maritime, freight and canals at the transport body, told the public audit committee: “I was not asked or instructed by anyone to continue to look for the document, but, accepting the interest that there is in it and understanding our obligations to try and be as transparent as we can, we did a further search in advance of preparation for this committee.
“This time, engaging with IT colleagues, there is some new software which allows for forensic searches – that’s not something that’s typically done because of the resource intensity of it – and that identified the submission of October 9,  which you have.”
When put to Ms Pacitti by the committee convener that a debate on the issue would be held in Holyrood the same day the document was released, Ms Pacitti said: “There was nothing choreographed around that – as soon as we found it, we alerted ministers to it and put it in the public domain at the earliest opportunity.”
The defence comes as Government officials were questioned on the taxpayer burden linked to Audit Scotland analysis that ministers intend to complete the Glen Sannox and Hull 802 no matter the cost.
Mo Rooney, the Government's deputy director of strategic commercial interventions, said: "Certainly we've continued to continually assess value for money, so there is no blank cheque. I mean, were there to be a suggestion of an increase, we would certainly be advising ministers in what the value for money position is. So it isn't a blank cheque.”
Meanwhile, the Scottish Government’s director of economic development Colin Cook refused to say if the Scottish Government would scrap the vessels.
“We’re determined to deliver these vessels, we understand that they’re vital for communities and that will be our focus,” Mr Cook said under questioning from Tory MSP Craig Hoy.