John Swinney is being urged to give an urgent statement to Parliament on the Hamilton probe into his predecessor Nicola Sturgeon following revelations in 'secret' papers published by the Scottish Government.

The call is being made by Scottish Labour deputy leader Jackie Baillie MSP after documents show that lawyers had concerns there was not sufficient distance between the inquiry and the Scottish Government when the probe was said to be independent of ministers.

Top legal figures raised fears relating to a secretariat set up to support James Hamilton's investigation into whether Ms Sturgeon as it was staffed originally by a single government official.

An unnamed female civil servant was appointed to a secretariat for the inquiry, continuing with her normal role in government alongside her work with Mr Hamilton. She was later joined by other civil servants who redacted parts of the report ahead of publication.

The lead civil servant briefed Mr Swinney and the Lord Advocate on aspects of the inquiry before the report was published, documents published on Saturday reveal.

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Mr Hamilton was tasked with investigating whether Ms Sturgeon broke the ministerial code in the wake of complaints made against Alex Salmond.

The former First Minister 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 concluding in his report published in March 2021 that she did not.

Senior Counsel James Mure KC told the Scottish Government he did not know if Mr Hamilton was aware the civil servant briefed Mr Swinney while working for his inquiry.

"This revelation seems to raise serious questions on the independence of the Hamilton inquiry and will raise fears that the Scottish Government sought undue influence on the inquiry without Mr Hamilton's knowledge," Ms Baillie told The Herald.

Scottish Deputy Leader Jackie Baillie (Image: Colin Mearns) "John Swinney should make an urgent statement to Parliament on the content of discussions between this civil servant and the now First Minister, and why such a clearly unacceptable arrangement was allowed to continue for so long."

She added: “This is just more evidence of a culture of secrecy and cover-up that rots at the heart of the SNP. Scotland deserves better.”

In a joint statement on Saturday SNP MSP Fergus Ewing and former SNP MP Joanna Cherry questioned the independence of the probe conducted by Mr Hamilton following the revelations, while separately Alba acting leader and former Scottish justice secretary Kenny MacAskill called for Ms Sturgeon to face a new probe.

“This casts a long shadow over [the Hamilton report's] findings some of which remain redacted. There is surely a prima facie case for the inquiry to be re run as this undermines public confidence in both the inquiry process and its conclusions," Mr MacAskill told the Herald on Sunday.

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As Ms Baillie called for a statement to Parliament by Mr Swinney other senior opposition MSP raised questions about how the inquiry was run.

“Even senior figures in the SNP are now asking how independent this inquiry really was if a civil servant was working for Hamilton while remaining in her original post and simultaneously briefing SNP ministers," said Scottish Conservative MSP Murdo Fraser.

"The SNP have a long history of misusing civil servants to their own end and they must now offer complete transparency over whether correct procedure was followed so that the Scottish public can trust the integrity of this investigation.”  

Scottish Lib Dem MSP Willie Rennie added: "I would be interested to know what James Hamilton makes of the revelation that the then Deputy First Minister was being kept abreast of his probe.

Irish lawyer James Hamilton (Image: Niall Carson) "This is a very tough situation for any civil servant to be thrust into. Both they and James Hamilton need to have been able to operate independently without fear or favour. 

"If this was not the case and any undue pressure was being exerted either directly or indirectly that would call into account the integrity of the probe."

Meanwhile, Mr Ewing has put down a written parliamentary question seeking the identity of the civil servant who headed Mr Hamilton's secretariat.

“I have no idea why the Scottish Government are so desparately intent on concealing the identify of the person seconded to head the secretariat for James Hamilton," he told The Herald.

"If the person appointed was a senior civil servant then the convention is that they should be named.

"It would be hard to envisage that they put a junior official in charge. Given the controversy around the release of their legal advice on Saturday, which shows the civil service...having a dual role to assist James Hamilton, and to continue to advise Ministers , this issue has become highly controversial in itself."

In legal advice to the Scottish Government dated March 2 2023, Mr Mure notes that the civil servant on the secretariat briefed the then Deputy First Minister Mr Swinney and also briefed the Lord Advocate on how Mr Hamilton might respond to ministers.

The discussion took place in a minute requesting the government cover Mr Hamilton's legal expenses.

The minute has not been published by the Scottish Government but Mr Mure refers to it in detail in his legal advice.

"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 writes.

"Thus [redacted] request that Mr Hamilton be permitted to engage independent legal advice and charge the costs to the Scottish Government was set out in an official minute to the DFM and Lord Advocate dated October 2020, and not in confidential correspondence addressed from and on behalf of the independent adviser."

Mr Mure adds: "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.

"In relation to the waiving of legal privilege, the minute appears to give ministers the writer’s personal insights into Mr Hamilton’s likely response to possible positions that ministers might adopt.

"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."

He continues: "I fully accept that it is not unusual for civil servants to perform a variety of functions which do not necessarily come into conflict.

"However, I sense that SGLD [Scottish Government Legal Department] has some concerns that the documents show a lack of proper separation between the ongoing work of ministers and civil servants, and the need for a scrupulously independent secretariat.

"For what it is worth, I share those concerns. If it were, or became, necessary to lay these matters out before the court, I consider that they would likely be the subject of comment by the Inner House."

The documents were published on Saturday after the Scottish Government lost a long running battle with the Scottish Information Commissioner relating to freedom of information requests on the Hamilton report.

A member of the public had requested evidence from the Hamilton inquiry but the government argued the information was not held by them but by the probe itself. The Information Commissioner ruled however the government did hold the information and should release it.

But the government then appealed the Commissioner's decision at the Court of Session - and lost the action.

After that decision the member of the public asked for the government to give him the legal advice behind its decision to appeal.

On September 9 this year, the Commissioner ruled that the Scottish Government had until October 26 to publish its legal advice or lodge an appeal at the Court of Session.

Much of the legal advice examines the relationship between the government and the inquiry, how separate the bodies were centring on the connection between a secretariat set up to support Mr Hamilton and the government.

A Scottish Government spokesperson said: “The decision to comply with the Commissioner’s decision and release the legal advice has been taken after careful consideration and does not set any legal precedent.   

“The material shows Scottish ministers took decisions based on appropriate analysis of the legal considerations. This included discussions with the Lord Advocate, who was content that there were proper grounds for appealing and who agreed with ministers that the decision should be appealed. 

“This was a complex and intricate point of FOI law, which the Court of Session’s judgement recognised as addressing a ‘sharp and important question of statutory interpretation’. The material reflects the thorough deliberation the Scottish Government gave to this matter.”