John-Paul Marks, who replaced Leslie Evans as permanent secretary in January, told MSPs it was “regrettable” the document confirming ministers were happy with the risks associated with the contract did not exist.
Ministers have been under intense pressure to explain why the decision to overrule concerns from ferry infrastructure owners CMAL when awarding the contract to Ferguson Marine Engineering Limited (FMEL) was not recorded appropriately, sparking allegations the Government may have broken the law.
The contracts for the Glen Sannox and unnamed hull 802 was signed without a full builder’s refund guarantee, which would have protected the Government from overspends and delays.
The ferries are now at least five years late and £150 million over-budget.
Scottish Labour MSP Daniel Johnson asked Mr Marks whether there may have been a legal requirement to appropriately record the decision under the Scottish Public Finance manual and the Public Finance and Accountability (Scotland) Act.
In response, the permanent secretary responded he would be “happy to take away your last point” to ensure he was “very precise in the legal requirement”.
Mr Marks added: “The decision back in 2015, the submission that went to ministers is on the website. I’ve read it, it sets out the risks, it sets out the mitigations and then ultimately a further document follows, which then records that ministers have agreed to award the contract.
"There is documentation that tracks the decision-making process, but I agree with you, it is regrettable.
“We need to be confident and ensure the recording … the minuting of those ministerial considerations is consistent and robust.”
Asked whether he agreed there was "something wrong" with the Scottish Government’s approach to transparency following recent scandals and the ruling that ministers must release legal advice around a second independence referendum, Mr Marks said there was “continuous improvement” around information management within the civil service.
He said he was “assuring himself” the Government’s approach to Freedom of Information was “robust”.
He said: “In 2021, we handled 4,000 Freedom of Information requests. That’s 25 per cent more than the year before.
"You reference the information commissioner, and when I have worked for over two decades in the civil service, the convention that legal advice is protected for ministers to create that private space for consideration of legal advice is a convention that is well established.
"This is not something unique to Scotland that somehow is being done here. This is a convention that is well understood.
"But we note the information commissioner’s judgement and will respond ahead of the deadline and ministers are giving it careful consideration.”
Mr Marks was appearing in front of the finance and public administration committee after his predecessor Leslie Evans refused to give evidence on her tenure as permanent secretary.
Defending her decision to turn down an invitation to give evidence, the new permanent secretary said the responsibility of the office passed to him when Ms Evans retired.
He told MSPs: “She left role on December 31. At that point she no longer holds the authority, the accountabilities or responsibilities of the role which transferred to me.
"She had some contractual agreement with regards to leave that was in lieu, but she finished and retired on December 31.
"It is for the office of the permanent secretary and for me in the role to appear.
"Leslie retired and therefore is no longer accountable to ministers and therefore does not appear as the permanent secretary for the Scottish Government after December 31.”