John Swinney is considering changes into how future investigations into alleged breaches of the ministerial code are set up in light of revelations in secret papers published by the government at the weekend.

Lib Dem MSP Willie Rennie pressed Mr Swinney over concerns raised in legal advice to the Scottish Government over how James Hamilton's inquiry into Nicola Sturgeon was handled.

The First Minister told Holyrood he would take on board concerns about the process for future investigations as he reformed the ministerial code.

"I want to make sure that ministers are held to the highest standards of probity and that we have the strongest and most robust arrangements in place for handling these matters," he said.

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"So I may reflect on the issues that Mr Rennie raises with me, because I recognise them to be substantial issues that have to be assured and command public confidence on an ongoing basis," he said. 

However, while Mr Swinney signalled the prospects of changes being made in future probes, he dismissed calls for a judge-led inquiry into his actions surrounding Mr Hamilton's inquiry into Ms Sturgeon.

The demands were made by Scottish Conservative leader Russell Findlay and Scottish Labour deputy leader Jackie Baillie following concerns over insufficient distance between the probe and the Scottish Government raised by lawyers which were revealed last weekend.

Scottish Labour deputy leader Jackie Baillie (Image: Gordon Terris) Concerns were revealed in Scottish Government legal advice, published on Saturday, relating to a long running freedom of information battle relating to the Hamilton inquiry.  Earlier today SNP minister Jamie Hepburn told MSPs that the legal case had cost the government around £118,000.

It emerged a secretariat was set up to support Mr Hamilton's work and that it was staffed by an unnamed female civil servant who corresponded with Mr Swinney during the investigation.

In the batch of documents Senior Counsel to the Scottish Government James Mure KC is seen raising concerns that the civil servant on the secretariat briefed Mr Swinney on Mr Hamilton's thinking ahead of the report's publication in March 2021 pointing out he did not know if Mr Hamilton knew of the civil servant's briefing role.

Former First Minister Nicola Sturgeon (Image: PA) "It appears to me somewhat unfortunate that more distance was not enforced between on the one hand the secretariat and those serving it, and on the other hand the Scottish Ministers and those advising them," he told the government on March 2, 2023.

Mr Mure pointed to a minute by the civil servant on the secretariat to Mr Swinney which related to a request for the government to cover any legal expenses he incurred during his work.

"The content of that minute provides a civil servant’s summary of the issues, rather than a request argued from the point of view of the independent adviser," he wrote.

"The minute appears to give ministers the writer’s personal insights into Mr Hamilton’s likely response to possible positions that ministers might adopt.

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"This again suggests a less than arm’s length and independent position. I can see that from one point of view [redacted] might appear to be the ideal person to brief ministers on such matters.

"However, I do not know to what extent Mr Hamilton was aware of this briefing role that [redacted] was performing. It appears to me that such briefing and process questions could have been dealt with by a civil servant not engaged in the secretariat, and that this would have provided further distance between ministers and the independent adviser."

The First Minister told Holyrood he would not hold an judge led inquiry into the matter insisting he had not seen the contents of Mr Hamilton's report until after it was published in March 2021.

Ms Sturgeon referred herself to Mr Hamilton in January 2019 in response to allegations she had misled Holyrood in relation to the inquiry into the botched investigation of harassment complaints against Mr Salmond. Mr Hamilton concluded in his report that she did not.

Mr Findlay accused Mr Swinney of being in charge of a "cover up".

He demanded to know if Mr Hamilton was aware of communications between the civil servant and Mr Swinney during the inquiry and to publish those communications.

James Hamilton (Image: Niall Carson) He said: “Here are the facts: a Scottish Government official was transferred to work for James Hamilton while he investigated allegations that Nicola Sturgeon breached the ministerial code. But we only now discover that during this time the official was passing information directly to Mr Swinney.

"She even drafted letters from Mr Swinney to Mr Hamilton – who she was working for. Hopelessly and fatally conflicted.

“The government then spent huge sums of money trying to keep all of this secret from the public. Despite his protests, the First Minister's fingerprints are all over this cover up.

 “So let me ask, were Mr Swinney’s communications with the seconded official done behind the back of Mr Hamilton? Mr Swinney has today admitted ‘some’ of the contact he had with the seconded government official. Will he publish details of all contact?

 “And finally, since all we’ve heard today is spin, will Mr Swinney agree to a judge-led inquiry to uncover the true extent of his actions?”

Mr Swinney rejected Mr Findlay's accusation of a cover up and that the government lacked transparency saying it had just published 101 pages of legal advice which in the First Minister's view should have been covered by "professional privilege".

Mr Swinney said Mr Hamilton was "in full control" of the whole process of the inquiry.

"I have absolutely no intention of commissioning a judge led inquiry into all of this business for the simply reason I have disclosed the information that the [Information] Commissioner requested," the First Minister told Holyrood.

Scottish Labour Deputy Leader Jackie Baillie accused Mr Swinney of being a "human shield for Nicola Sturgeon" during the parliamentary inquiry into the Scottish Government’s handling of harassment complaints.

She warned that without greater transparency, the revelation over the secretariat could reduce trust in other public inquiries where civil servants were seconded in this way.

She added: "Given the need for integrity and good governance, I echo the call for a judge led inquiry. The First Minister should really agree, unless, of course, he has something to hide."

Mr Swinney hit back accusing Ms Baillie of being prepared to "sully people's character".

In his statement to Holyrood the First Minister defended his handling of the inquiry into Ms Sturgeon.

"I formally initiated the process. I sponsored the process within government. But in setting out that factual information that parliament has known about since 2020, I want to make one point crystal clear: the first time I learned of any of the contents of James Hamilton’s report was when he sent it to ministers on 22 March 2021," Mr Swinney told MSPs.

Mr Swinney told MSPs that his contact with the civil servant on the secretariat concerned Mr Hamilton's request that the government would pay for any legal advice he sought and in relation to communications over parliamentary business.

"As the sponsoring minister, these practical issues rightly came to me for agreement because they had nowhere else to go," he said.

He added: "James Hamilton is an independent commissioner of impeccable reputation and integrity.

"The person who supported him as the secretariat was a non-political career civil servant. Questioning the independence and integrity of James Hamilton and of a civil servant who cannot publicly defend themselves, is unwarranted, unfair and unsupported by the facts."

Earlier the minister for parliamentary business Jamie Hepburn was asked the identity of the civil servant seconded to the secretariat.

He said: "It would not be appropriate to reveal that name. The support was provided by a career civil servant of a seniority below that of the senior civil service grade — that is, by a junior Scottish Government official. 

"We need to bear that in mind in providing any information, because we have to adhere to data protection principles. That is why the individual’s name rightly will not be made public."

During the debate Mr Swinney said the civil servant who joined Mr Hamilton's secretariat was not a special adviser.

He also denied opposition parties' claims the government had wasted public money appealing a ruling of the Scottish Information Commissioner in the Court of Session saying legal advice ministers received suggested they had a reasonable chance of success.

The legal battle with the Commissioner dates back to April 2021 when a freedom of information (FOI) request was made by a member of the public to obtain all evidence submitted to the Hamilton inquiry into whether Sturgeon breached the ministerial code when she was first minister.

Ms Sturgeon had referred herself to Hamilton, the independent adviser on the ministerial code, in response to allegations she had misled Holyrood in relation to the inquiry into the botched investigation of harassment complaints against Mr Salmond.

The information commissioner ordered ministers to divulge the information, arguing that the evidence collected by Mr Hamilton and held by the government should be subject to FOI legislation.

In March last year, Mr Swinney, after taking legal advice, decided to appeal against the commissioner’s decision at the Court of Session on the grounds that the government did not hold the information, claiming it was in a restricted part of its information management system only accessible by Mr Hamilton and his team.

The Scottish Government lost the action leading to the member of the public to submit a new FOI seeking the legal advice on which the decision to appeal was based.

The Commissioner ruled in September the Scottish Government should release the advice or appeal to the Court of Session by a deadline of October 26, last Saturday.

Ministers decided against a further appeal and published the legal advice last Saturday.