Nicola Sturgeon has denied her government staged a cover-up over its decision to hand a scandal-hit ferries contract to a shipyard owned by an independence supporter after it admitted key documents “cannot be located”.

The First Minister said it was “regrettable” that there was no paper trail showing why her administration had handed the contract to Ferguson Marine after ferry chiefs warned the award was too risky and asked for it to be withdrawn.

She argued that her government had provided lots of other information but “this particular piece of written evidence” was not available.

But the Tories said it was “inconceivable” that there was nothing in the Scottish Government’s records to show why SNP ministers pressed ahead without a full refund guarantee, a standard clause in shipbuilding contracts.

The ferries’ cost has since spiralled from £97 million to £250 million and their construction is running five years late.

When the contract was awarded in 2015, Ferguson Marine was owned by Jim McColl, an engineering tycoon who supported independence in the previous year’s referendum. However, the SNP later nationalised the shipyard.

Ms Sturgeon’s intervention came the day after Scotland’s auditor general expressed frustration that SNP ministers failed to provide any records to his inquiry showing why they approved the contract.

‘There is no cover-up’

Stephen Boyle told Holyrood’s public audit inquiry there was “no documentary evidence” why they had decided to overrule ferry company Caledonian Maritime Assets Ltd (CMAL) by pressing ahead without a repayment guarantee.

He said the lack of any record of ministers’ discussions was “so unusual in the scale of this contract” and argued for a “fuller review” of what had happened.

In a statement issued on Thursday, the Scottish Government said: “A thorough search has been conducted and the paperwork/documentation cannot be located.”

Asked if the absence of the key documents was down to “incompetence or a cover-up”, Ms Sturgeon replied: “There is no cover-up. There is clearly a key point of decision making that has not been recorded in the way it should have been. That is regrettable, but there is no cover-up around this.”

Speaking at the SNP’s council election manifesto launch in Greenock, less than four miles from where the vessels are being built, Ms Sturgeon said there was “no suggestion” from Mr Boyle that any documents had been withheld.

She said: “It was simply that this particular piece of written evidence, this particular decision hadn’t been recorded. That is regrettable – I’m not trying to diminish the importance of that.

“But anybody can go on to the Scottish government website and look at the sheer quantum of paperwork recording our decisions around this issue, other than that.”

‘Murky affair’

She pledged to answer the public audit committee’s questions about the scandal “to the very best of my ability”.

Mr McColl has alleged the contracts were rushed through before the specifications were finalised to deliver a political boost to Ms Sturgeon at the 2015 SNP conference and the following year’s Holyrood election.

Graham Simpson, the Scottish Tories’ Shadow Transport Minister, said: “In this day and age, it’s almost inconceivable there is not an electronic trail of how this fateful decision was made, even if there is no paper copy.

“And Nicola Sturgeon has the audacity to claim she’s being open and transparent on this scandal. It’s clearer than ever we need a public inquiry to get to the bottom of this murky affair.”