SCOTTISH Police Authority chair Andrew Flanagan finally quit yesterday after months of criticism about secrecy at a watchdog he led for less than two years.

Mr Flanagan announced his resignation after a series of damaging revelations in the Herald about a lack of transparency at the troubled organisation.

Justice Secretary Michael Matheson said he was grateful to Mr Flanagan for his "significant contribution to policing" and noted that the chair had acknowledged making mistakes.

The SPA was created to provide oversight of Police Scotland and helps approve a £1bn budget for policing north of the border.

However, the watchdog has itself become the story recently over a botched governance rethink tied directly to Mr Flanagan.

Amongst the many changes implemented, the SPA moved to private committees and restricted publication of board papers until the day of a meeting.

In February, this newspaper revealed that Moi Ali had resigned from the SPA board after falling out with the chair on the two proposals.

After Ms Ali publicly dissented from these recommendations, Mr Flanagan sent her a private letter complaining about her decision to speak out. She resigned weeks later.

The Herald then disclosed that Mr Flanagan failed to share a letter by Derek Penman, Her Majesty's Inspector of Constabulary, that was critical of the governance plans.

Both controversies reached Holyrood and were examined by two parliamentary committees, whose members were angry about the treatment of Ms Ali and the HMICS row.

In a letter to Justice Secretary Michael Matheson, the Public Audit and Post-legislative Scrutiny committee concluded that the chair had behaved in an “inappropriate manner” towards Ms Ali and claimed it had been “unacceptable” not to share the letter. MSPs on a second committee piled pressure on Mr Flanagan by saying they did not have confidence in him.

He later apologised to Ms Ali, but the criticism continued and he announced his intention to stand down yesterday. In a letter to Matheson, he wrote:

“Recent events have focussed on my disagreement with a board member and concerns that by discussing with the Board issues raised by HMICS rather than copying his letter this was indicative of a wider lack of transparency, which of course is not the case.

“To remedy these issues, I have apologised to the former board member and put in place changes to the governance processes of the SPA to ensure there can be no perception of a lack of openness.”

However, Mr Flanagan wrote that the “prolonged and continued debate” in the media and in Parliament was “not helpful” to the SPA or policing and was proving to be a “distraction”.

Mr Flanagan continued: “In addition, the debate has become quite personalised and has impacted on me and my family. This is not something that I wish to endure further. I have therefore taken the decision that it would be in the best interests of policing if I were to step down from my role as Chair of the SPA.”

He added that he would be willing to continue as chair until a successor is found and an “orderly hand-over” could take place.

In a statement, Ms Ali said: “It is right that one of Scotland's biggest and most important public bodies has at its helm someone of the utmost integrity, who is genuinely committed to openness, transparency and diversity. Andrew Flanagan's actions in a number of areas have called into question his judgement and his commitment to public service values. His decision to resign from the SPA is the correct one.”

Liberal Democrat MSP Liam McArthur said: "Andrew Flanagan has taken the right decision in the interests of the SPA. However, serious damage has already been done to the reputation of the organisation. For that, the SNP government must accept its full share of the blame, given their botched centralisation of policing.”

Scottish Green MSP John Finnie said: “Andrew Flanagan has made the right decision, albeit at the wrong time. Rather than creating a period of uncertainty, Mr Flanagan should have resigned weeks ago when it was crystal clear that two of the Parliament’s committees questioned his ability to lead this important organisation.”

Mr Matheson said: "I am grateful to Andrew Flanagan for his significant contribution to policing, having become chair at a key time for the sector and brought a more strategic focus to the oversight of this key public service.

"However, he has acknowledged that mistakes have been made. He has offered a full and very public apology and made clear changes to transparency and governance in light of the concerns raised.”