Permanent Secretary of the Department for Constitutional Affairs

Allan was the first Permanent Secretary of the Ministry of Justice, having been the last Permanent Secretary of the Department for Constitutional Affairs from which it was created, together with the addition of HM Prison Service and the Office for Criminal Justice Reform, which were taken from the Home Office. Allan served in both of these roles from 1 August 2004 to 15 November 2007. An historical attribute of the role of Permanent Secretary of the Ministry of Justice and its predecessor departments (which included the Lord Chancellor's Department) is that it carries with it the role of Clerk of the Crown in Chancery, an ancient Office, which entails responsibility for overseeing the creation of Letters Patent under the Great Seal, discharged by the Crown Office, itself based in the House of Lords. The Clerk of the Crown in Chancery also has various other responsibilities, including the State Opening of Parliament, and the Prorogation of Parliament. Until the role of the Lord Speaker was carved out of that of the Lord Chancellor, the Clerk of the Crown in Chancery occupied one of Parliament's most prestigious rooms, adjacent to those of the Lord Chancellor. Allan was the last Permanent Secretary and Clerk of the Crown in Chancery to enjoy this splendid room, which he agreed to surrender to the House Authorities so that they could provide suitable accommodation for the newly created Lord Speaker. The only alternative would have been for his political master, the Lord Chancellor, to have given up his room.

On 17 October 2006, Allan submitted oral evidence to the Constitutional Affairs Committee. He was questioned on the 're-organisation of the centre of the Department' (for constitutional affairs) which he stated in his annual report. Allan was asked what he thought were the key changes he had made to the department since his two years in the post. He stated that the key changes to the Department for Constitutional affairs were structural. Allan admitted the department faced big challenges and that there was a lot still to be done. Allan was also questioned over the 'chaos' of the Oracle system (a computer system used by the department).^[2]

On 6 February 2007 Allan attended a meeting with the management board for the Information Commissioner's Office (ICO). His duty was to brief the board about the Department for Constitutional Affairs' approach to information rights and the ICO itself.^[3] In this meeting Allan recognised inadequate pay as being a key issue in the ICO and across the Department for Constitutional Affairs.

On 4 July 2007, before the Constitutional Affairs Committee, Allan was asked whether he had written an article for MP Vera Baird in The Times. He denied the accusation.^[4]

Chairman of the Joint Intelligence Committee (JIC)

On 15 November 2007 he was appointed Chairman of the Joint Intelligence Committee and Head of Intelligence Assessment. Allan's role was to collect intelligence from the Security Service, MI5, the Secret Intelligence Service, MI6, GCHQ and other sources of intelligence, and present them to ministers as threats developed.^[5] He had access to the Prime Minister at all times and also top secret US and UK intelligence reports.

Allan was appointed Knight Commander of the Order of the Bath (KCB) in the 2012 New Year Honours.^[6][7]

Independent advisor on ministerial standards

In November 2011 he was appointed by David Cameron as the Prime Minister's independent advisor on ministerial standards.^[8] In 2012 he said to a public administration committee of MPs that if ever he were "bypassed", he would step down.^[9] He resigned from the post on 20 November 2020 after PM Boris Johnson backed Priti Patel following a report Allan had compiled that concluded that Patel's approach "amounted to behaviour that can be described as bullying"^[10] and that she had "not consistently met the high standards expected of her".^[9] Christopher Geidt also resigned as ethics adviser under Johnson.