Sir Peter will leave office “in good heart” after what he said was a “vibrant and challenging” time, that saw him serve as Scotland’s top mandarin during the SNP government’s staging of the independence referendum.
However, his tenure as Permanent Secretary has at times been dogged by opposition allegations that he had gone “native” in his relationship with the nationalist administration.
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He also drew criticism for posting an online diary that offered an insight into his struggles with his golf swing, his dietary habits, enthusiasm for gardening and grasp of the minutiae of domestic trivia.
Opposition politicians said other extracts from the diaries also breached civil service neutrality because they were too pro-independence.
Sir Peter, who reaches the retirement age of 65 this year, said he would leave his post at the end of June, which he said would allow his successor to settle before the Holyrood elections in May 2016.
Alex Salmond said Sir Peter handled the referendum process and talks with the UK government “particularly well”, as an “outstanding public servant”.
But opposition politicians last night called for a “shake-up” of Scotland’s civil service.
Sir Peter, who earns about £180,000 a year, was cleared of a breach of the civil service code over an internal briefing advising that the referendum debate had left “the status quo … lost in the mists of time”.
Some politicians have continued to question his impartiality, including Sir Bernard Jenkin, Conservative convener of Westminster’s Public Administration Committee, who asked whether he could serve another administration if the SNP is voted out in 2016.
Sir Peter denied acting as a “cheerleader” for independence after he told the Commons committee he had raised no concerns with SNP ministers that the white paper on independence could have compromised civil service neutrality.
Liberal Democrat MSP Tavish Scott yesterday suggested Sir Peter presided over a politicised civil service and the promotion of SNP policy with the launch of the white paper in late 2013.
Mr Scott said: “The Scottish civil service needs a shake-up. If they are to be impartial and above reproach, we cannot see repeats of the infamous independence white paper.
“That was an SNP political manifesto and contrary to the values of an independent civil service. Change at the top was needed and Scotland will look for a new approach from a new permanent secretary.”
A spokesman for the Scottish Conservatives, welcoming Sir Peter’s departure, said: “We need to draw a line underneath that period and given that, Sir Peter’s decision to leave before a potential change of government in 2016 is the right one.”
Sir Peter, who said he would pursue another position in public service, maintained he had expressed no view on Scottish independence and leaves the top job in the civil service “with our values intact”.
He said: “A person cannot do these jobs forever and I want to enable my successor to come into post in good time for the run-up to the Scottish Parliament elections in May 2016.
“I am confident that my successor will find the civil service in Scotland in good heart.
“This has been a vibrant and challenging period. We have come through with our values intact, with strong capability and in a spirit of partnership across Scotland, and with the UK government and its agencies.”
“I hope to contribute to the development of public service here and in other settings in the years ahead. I will make an announcement on my plans at the end of June.”
First Minister Nicola Sturgeon praised Sir Peter’s contribution to public life during an “immensely exciting and dynamic time”.
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