THE Justice Secretary has been accused of misleading parliament after new evidence challenged his account of a crucial meeting about Scotland’s absentee Chief Constable.

Scottish Labour said Michael Matheson should now “consider his position”.

Mr Matheson’s version of events was called into doubt by the former chair of Police Scotland’s oversight body this morning.

Andrew Flanagan, the former chair of the Scottish Police Authority, said Mr Matheson told him it would be “bad decision” per se to let Chief Constable Phil Gormley return to duty.

Mr Flanagan told MSPs that the Justice Secretary told him in the first of two meetings on November 9 that he thought Mr Gormley’s return could destabilise Police Scotland.

It was only in a second meeting, an hour later, that Mr Matheson - now with three officials alongside him - changed tack and focused on the “process” behind the decision instead.

Mr Flanagan’s account, to Holyrood’s public audit committee, is potentially deeply damaging to Mr Matheson, as it could imply the Justice Secretary misled parliament.

Mr Gormley’s lawyer has accused Mr Matheson of acting “unlawfully” in intervening in a decision of the SPA, which is supposed to autonomous.

Mr Gormely's legal team said the new evidence was of "serious concern".

Earlier this month, Mr Matheson insisted his concern had been issue with the process behind the decision, not the decision itself, and he had merely asked the SPA to “reconsider”.

He told parliament: “This is not about an operational decision-making matter, but about the SPA’s process in making a decision… I am very clear that it is not the outcome of the SPA’s future decision on the chief constable’s leave situation but the process that the SPA goes through in making it that needs to be robust and defendable.”

The row goes back to the SPA’s decision on November 7 to allow Mr Gormley to return to work, after a period of special leave, despite a series of bullying claims against him.

The SPA decided he should, but did not consult the watchdog investigating the claims or the acting Chief Constable in advance of doing so.

Two days later, Mr Flanagan had a one-to-one meeting with Mr Matheson in the latter’s office at Holyrood, and told him of the board’s decision.

Mr Flanagan told MSPs: “I explained the circumstances and he told me that he thought it was a bad decision.

"It was clear to me that he did not want the chief constable to return at that point.

"We had a discussion about the stability of the senior team, because that was a consideration that the SPA had had.”

Mr Flanagan said that after an hour’s break in which he attended a committee, he was was recalled to Mr Matheson’s office, where three officials had joined the Justice Secretary.

He said: “It was clear that the Cabinet Secretary was still very unhappy, but he changed to discuss the process rather than the decision itself.

“I reminded him of his comment earlier that it had been a ‘bad decision’. He told me not to bother with that. We then went on to discuss some of the process itself.”

He said the meeting focused on what the independent watchdog thought of Mr Gormley returning and how to ensure the wellbeing of Mr Gormley’s accusers could be protected.

Mr Flanagan said Mr Matheson said the process was “deficient” without these issues being clear, and Mr Flanagan relayed his “adverse reaction” to the rest of the SPA board.

The board swiftly reversed its decision to reinstate Mr Gormley, who remains on leave.

Mr Flanagan said he was not formally directed to stop Mr Gormley’s return - which would have been an overt political decision - but he did feel he had no choice but to think again.

In more useful testimony for the Justice Secretary, Mr Flanagan said he had not expected the meeting with Mr Matheson and his officials to have been minuted - a bone of contention for the opposition parties.

In later evidence, other SPA board members admitted there was no hard and fast plan in place to ensure the welfare of officers, only a “process” that could lead to a plan.

The SPA has also decided not to tell the independent watchdog or acting chief constable Iain Livingstone or Mr Gormley’s proposed return until after telling Mr Matheson first.

SNP MSP Alex Neil asked Mr Flanagan whether he had "lied" to Mr Livingstone he deflected a query about Mr Gormley’s return - after the SPA had decided in favour - with a text message saying “deliberations were ongoing”.

Mr Flanagan said: "No, I don't think I did."

Mr Neil added: “The amnesia around the Scottish Police Authority is beyond belief.”

Mr Neil also excoriated the whole SPA board’s handling of the matter, saying its non-executive directors had “utterly failed in their duty” and should fall on their swords.

He said the SPA’s recent performance had been a “pantomime”.

At First Minister’s Questions, Nicola Sturgeon said Mr Matheson had acted “entirely appropriately” and in the interests of the people of Scotland by quizzing the SPA’s decision.

Her spokesman later denied the Justice Secretary had misled parliament by omission.

A spokesperson for Mr Gormely's legal team said: "The Chief Constable’s professional reputation, career and welfare have been eclipsed by a public battle of wills between the SPA and the Scottish Government.

"It demonstrates that the present system for investigating complaints against the Chief Constable is unworkable and requires a fundamental review.  

"It is hard to see how any fair process can now follow given such public disagreement.”

Mr Gormley has consistently denied any wrongdoing.

Labour justice spokesman Daniel Johnson said: “Yet again new details have emerged about the Justice Secretary’s meetings with the SPA that he had previously failed to disclose.

“It turns out, that in contradiction to what Michael Matheson told Parliament, the Justice Secretary initially told Mr Flanagan it was a ‘bad decision’ to reinstate Phil Gormley.

“Mr Matheson’s concerns around process were only raised in the second meeting that day.

“Mr Matheson misled Parliament, telling the chamber that he had only raised concerns about the decision-making process, not the decision to reinstate Phil Gormley itself.

“It is clear Michael Matheson behaved inappropriately for a Cabinet Secretary, repeatedly obscuring the true details of exactly what happened in his meetings with Andrew Flanagan, and he now must consider his position in the cabinet.”

After the committee meeting, Mr Flanagan insisted to the media that Mr Matheson had used the words “bad decision” about the return of Mr Gormley, and had never raised issues of process, in the pair’s initial 15-minute meeting on November 9.

He said: “He [Mr Matheson] thought it [Mr Gormley’s absence] was a stable situation, which I didn’t think, and it could become destabilised by the return of the Chief Constable.”