The Scottish Government’s handling of freedom of information (FOI) requests is under fresh scrutiny following claims of information being withheld for political reasons.

It follows research suggesting that documents were removed from an FOI response at the behest of deputy first minister John Swinney.

The allegations, brought to light by lecturer and journalist James McEnaney, are being investigated by the Scottish Information Commissioner (SIC) Daren Fitzhenry.

At First Minister’s Questions on Thursday, Nicola Sturgeon was questioned on the issue by Labour MSP Rhoda Grant.

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And earlier in the day at Holyrood, the Scottish Conservatives called for parliamentary business minister Joe FitzPatrick to return to the chamber to answer claims he “misled” MSPs during a debate on the matter last year.

The involvement of politically-appointed special advisers (SPADs) in the handling of FOI requests from journalists has caused friction in the past.

Last year, 23 journalists, including trade union representatives from STV News and the BBC, signed an open letter raising a number of complaints about the handling of information requests from members of the media.

Part of the SIC’s investigation into the government’s conduct will explore whether information requests from journalists are treated differently to those from other people, and if so, does it restrict or reduce journalists’ entitlement to information compared to other requesters.

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Scotland’s FOI watchdog also said it will examine the role of special advisers in the request-handling process and probe if politically-sensitive requests are handled under different procedures to others.

The commissioner’s plans to assess government handling of FOI is detailed in a February 2 letter to FitzPatrick which can be read in full at the link below:

The First Minister said oversight of FOI requests by ministers and the involvement of SPADs was “very routine” and had been the case “right back to before we were in office”.

The Scottish Government currently has 14 special advisers, the joint-highest total since devolution.

Mr McEnaney published a series of tweets featuring screenshots of internal government emails he had obtained, after being denied them for months.

The emails detail the involvement of deputy first minister and his SPAD McAllister in the crafting of an FOI response to Mr McEnaney concerning issues around education.

One such message from an unnamed private secretary to Swinney reads: “DFM is content for this to go but thinks it would be better to see if we could not release the material relating to Prince Charles or his PS [redacted].

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“He specifically referenced documents 20, 24, 25, 26 as ones he’d prefer were not released.”

Mr McEnaney tweeted in response: “It doesn’t (or, more accurately, shouldn’t) make any difference what a minister would ‘prefer’ or what a SPAD wants.

“That’s not how FOI is supposed to work.”

The revelations were raised in the chamber by Rhoda Grant MSP, who said: “The First Minister appears to be aware that her government and their special advisers are holding back material from FOIs that could cause them embarrassment.

“Does she therefore believe that saving their own blushes is more important than transparency, and indeed, the law?”

Sturgeon responded: “FOI requests are handled by Scottish Government officials. They seek comments from relevant parts of the Scottish Government and consider whether ministerial clearance should be sought.

“That’s entirely appropriate because the legal duty to comply with FOI legislation lies with Scottish ministers. I think it is schedule one, part one, paragraph one.

“Scottish ministers are subject to FOI and at all times FOI requests are handled in line with the legislation, and that includes whether or not particular exemptions are applied.”

A spokesman for the First Minister later added: “It is very, very routine for ministers to have oversight of information being released by the Government.

“Special advisers are civil servants and have always been involved in the FOI process, right back to before we were in office. That has always been the case.”

The issue had already been brought up in the Holyrood chamber earlier on Thursday, when a Conservative MSP suggested FitzPatrick may have misled parliament when questioned on FOI last summer.

When asked in June whether information requests were being screened for potential political damage by special advisers, the parliamentary business minister replied: “No, requests are all prepared by Scottish Government officials.

“Special advisers have a role in assessing draft responses for accuracy.”

Edward Mountain told MSPs: “We now know that the answers given by Mr FitzPatrick to the Scottish Parliament are not true.

“The evidence suggests that special advisers are routinely involved in the freedom of information process for political purposes and John Swinney himself is suppressing documents when it suits him.

“Mr FitzPatrick categorically denied this on the floor of the Scottish Parliament.

“Joe FitzPatrick must return to the Scottish Parliament immediately and explain these responses.”

The Tory MSP added: “It appears this may well be a breach of the ministerial code of conduct.

“It is entirely unethical for a Scottish minister to mislead the Scottish Parliament.”