SCOTTISH Police Authority (SPA) chairman Andrew Flanagan has apologised for his treatment of a former board member but told MSPs he will not quit.

Andrew Flanagan said he “greatly regretted” his treatment of Moi Ali, who has accused him of bullying and effectively forcing her out of the organisation.

Flanagan has come under pressure to resign following an accusation of bullying and serious concerns over transparency at the police watchdog.

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He told Holyrood’s Justice Sub-Committee on Policing that while there had been some “reputational damage” to the organisation, it would do more damaging if he were to go.

The controversy centres around a letter sent by Flanagan to board member Ali, who resigned from the board after publicly objecting to holding meetings in private.

Flanagan expressed his dissatisfaction and suggested it would not be fair for her to continue to attend committee meetings – a move Ali described as “bullying”.

He told MSPs he had now written to Ali offering “my full and unreserved personal apology”, and insisted he had “a deep and sincere regret about how things unfolded”.

The apology came after Holyrood’s Public Audit Committee wrote to Justice Secretary Michael Matheson on Friday, branding Flanagan’s behaviour as “unacceptable”.

“That made me reflect on where we were. I have put my version of events to them (the Public Audit Committee), they have listened to Moi Ali’s version of events,” Flanagan said.

“Their conclusion is they believe she was right and I have to accept that, and therefore it was a natural consequence that I should apologise in writing to Moi.”

Flanagan said his apology had been written “on Tuesday or so” but Ali took to social media to state she had received it by email just over an hour before his appearance before MSPs.

Asked if he accepted there had been “reputational damage to SPA that it may not recover from”, he said: “I think we can recover from it, I think there has been some damage there.

“I think my apology to Moi is a start of that process, it is not the end of the process. I have been referred to as bullying – that is not an accusation I do accept. I have written a poorly-worded letter in haste, and I regret that deeply, but I don’t think it amounts to bullying.”

Flanagan has also come under fire for failing to pass on to other board members a letter sent to him by Derek Penman, HM Chief Inspector of Constabulary in Scotland (HMICS), questioning governance arrangements at the SPA and the decision to hold some of its meetings in private.

He told MSPs he had put in place an “automatic process” to circulate formal communications to all board members and confirmed the board and its committees will meet in public “while retaining the need to hold some items in private where necessary”, with papers published “well in advance”.

On his own position, Flanagan said he had the “unanimous support of board”, stating that in his two years as chair “there is more that I have got right than wrong”.

His future was challenged, with MSP Stewart Stevenson referring to his own resignation as transport minister in 2010.

“The biggest of people will always put the interests of the organisation of which they are part above their personal considerations should they be part of the decision-making,” he told Flanagan. “I simply invite you to take the same position as I took in 2010.”

Scottish Tory shadow justice secretary Douglas Ross said: “If he won’t walk, the Scottish Government should consider taking action.”