Doubt has been cast over the independence of the inquiry into whether Nicola Sturgeon broke the ministerial code after revelations a secretariat set up to support the probe was staffed by Scottish Government civil servants.

The information emerged in documents published yesterday by the SNP administration into a long running freedom of information case relating to James Hamilton's probe into the former first minister.

Ms Sturgeon referred herself in January 2019 to Mr 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 her predecessor Mr Salmond.

Mr Hamilton's report, published in March 2021, ruled that Ms Sturgeon did not breach the code.

But there are now concerns over how independent the inquiry was of government after a batch of secret documents released by the Scottish Government reveals lawyers feared there was not enough distance between ministers and civil servants and the Hamilton probe.

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The issue has come to light in legal advice the Scottish Government was given into whether or not to appeal a freedom of information ruling.

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.

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

The secretariat was headed by an unnamed Scottish Government civil servant who continued to work for the government alongside her role with Mr Hamilton. The document also reveals she briefed the government on aspects of the inquiry.

The Scottish Government lost its appeal against the Information Commssioner at the Court of Session (Image: PA) The legal advice published on Saturday shows lawyers raising concerns over a lack of distance in the relationship.

In an opinion dated March 2 2023, senior counsel James Mure KC notes the civil servant on the secretariat at one point discussing the case with John Swinney, then Deputy First Minister, and the Lord Advocate in a minute requesting the government cover Mr Hamilton's legal expenses.

References to who the civil servant appointed to the secretariat are redacted.

Mr Mure points out he is not aware if Mr Hamilton knew that the civil servant heading the secretariat was also briefing ministers.

"While I understand that there may be a standard approach where civil servants are serving an independent inquiry but also engaged in some liaison role, I have seen no formal note outlining such an approach.

Former First Minister Nicola Sturgeon giving evidence to Holyrood on the Scottish Government's mishandling of complaints against her predecessor Alex Salmond. (Image: JEFF J MITCHELL) "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.

"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 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 also reveal that the unnamed female official was seconded to the role on a part time basis while continuing to work for the Scottish Government, using her government email address for both roles.

James Hamilton (Image: Niall Carson) More Scottish Government civil servants later joined the Hamilton inquiry secretariat ahead of the publication of his report to carry out redactions, the document also reveals.

It states: "The secretariat to Mr Hamilton comprised a single official – described as the “the secretary” below – except for a short time prior to publication of his report when several officials from the Organisational Continuity Team were seconded to the secretariat to take forward necessary redactions from his finalised report before publication."

It adds: "The secretary role was not a full-time one and would not have merited that. The official concerned continued – with an adjustment of workload – to work in the team leading on [redacted]

It continues: "Counsel was also asked to consider the day-to-day practical arrangements that the secretary used to manage the inquiry’s work and, subsequently, to store the information.

"The secretary used her normal Scots Outlook account for work both as secretary to the inquiry and for other SG activity. As is not unusual several SG officials had permissions to access that mailbox, providing contingency to access the mailbox for example if there were an urgent business requirement in the case of unexpected absence.

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"We are not aware that anybody accessed the mailbox during the period when information about the inquiry would have been present in mailbox. It is, however, theoretically possible that it could have been accessed by other SG officials."

In a note weighing up options to appeal or not the Scottish Government notes that appealing "may invite public scrutiny of the details of secretariat arrangements in this case, and in similar other cases."

It adds: "In reaching its decision, the Court may request that the Scottish Government share material explaining the set up and operation of the Hamilton inquiry. This may invite public scrutiny of the details of Secretariat arrangements in this case, and in similar other cases."

Summarising concerns against appealing the decision of the Office of the Scottish Information Commissioner's a Scottish Government briefing also notes that inaccurate information had been previously given to the watchdog before again underlining concerns relating to the independence of the inquiry body.

It states: "The concerns of SGLD [Scottish Government Legal Department] are (i) what we advised OSIC happened was not wholly accurate and (ii) whether the secretariat had proper separation between the work of Ministers to ensure the necessary degree of independence for the Secretariat.

"In relation to (ii), a full precognition exercise has not yet been undertaken to examine these issues and in the time available a full consideration of whether, in hindsight, the necessary degree of independence was achieved has not been possible.

"As such, there is a risk of presentational issues arising on these matters but also an appeal may not be the best context in which to corporately reflect on these matters."

The lawyers' concerns last night prompted Kenny MacAskill, acting leader of the Alba Party, to call for a new inquiry into whether Ms Sturgeon broke the ministerial code saying the advice provided by Counsel undermined the Hamilton probe.

“The Scottish Government have had to be dragged kicking and screaming by the Freedom of Information Commissioner to this point," said Mr MacAskill.

“They have gone to great lengths to avoid publishing this information. Now we know why. They were warned by their own lawyers that there was insufficient distance between the Government and what was meant to be an independent inquiry.

“This casts a long shadow over its 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.”

In a Joint Press statement, SNP MSP Fergus Ewing and KC and former SNP MP Joanna Cherry  also raised concerns over the independence of the Hamilton inquiry.

They said: "The revelation that the civil servant who provided the Secretariat to the inquiry, was at the same time, continuing to brief and advise Scottish government ministers about aspects of the investigation, calls into question whether this was ever an independent inquiry at all."

The Scottish Government said the document showed that it took the decision to appeal over the Information Commissioner's ruling based on "appropriate analysis of legal considerations".

A 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."

In his report published Mr Hamilton said the First Minister had not violated the ethics code over her conduct in relation to the investigation into Mr Salmond.

Referring to the four aspects he investigated, he concluded: "I am of the opinion that the First Minister did not breach the provisions of the Ministerial Code in respect of any of these matters."

However, Mr Hamilton's report said she had given MSPs an "incomplete narrative of events" by failing to tell them about a key meeting, and it was only because he deemed it "a genuine failure of recollection" and "not deliberate" that it did not amount to a breach of the code.