The top civil servant in the Treasury has left his post after six years, citing the new Chancellor’s preference for fresh leadership.

Sir Tom Scholar, who has worked in the Civil Service for three decades, said he would be cheering the department on “from the sidelines” following his departure as permanent secretary.

The move – which will be seen as a steer away from the so-called “Treasury orthodoxy” criticised by Liz Truss – prompted a backlash from Lord Macpherson, who previously held the top role in the department.

The peer said the senior mandarin’s experience would have been “invaluable” in the coming months.

“Tom Scholar is the best civil servant of his generation,” he said.

“Sacking him makes no sense. His experience would have been invaluable in the coming months as Government policy places massive upward pressure on the cost of funding.

“As Gordon Brown used to say ‘they’re not thinking’.”

Dave Penman, general secretary of the FDA union, which represents civil servants, claimed an “ideological purge of permanent secretaries” was underway.

“Liz Truss had a chance to reset the relationship between ministers and civil servants, yet even before she was officially elected, her team were briefing against the Treasury permanent secretary Tom Scholar,” he said.

“Now, on the very afternoon that she wrote to civil servants saying that ‘our world leading civil service is the ace up the sleeve of any prime minister’, an ideological purge of permanent secretaries has begun.”

A successor will be appointed shortly, the Treasury said.

In the meantime, Beth Russell, director general of tax and welfare, and Cat Little, director general of public spending, will lead the department as acting permanent secretaries.

Sir Tom said: “The Chancellor decided it was time for new leadership at the Treasury, and so I will be leaving with immediate effect.

“It has been the privilege of my career to lead this great institution since 2016. I wish the Treasury all the best for the times ahead, and I will be cheering on from the sidelines.”

Kwasi Kwarteng said Sir Tom had helped steer the Treasury and Government through “many economic challenges” – from the financial crisis to the Covid-19 pandemic, and he leaves the Civil Service with “the highest distinction”.

Cabinet Secretary Simon Case, who has been asked by Mr Kwarteng to begin the search for the senior mandarin’s replacement, described him as a “steadfast and loyal colleague”.

“Both personally, and on behalf of the whole civil service, I would like to thank Tom for his remarkable public service and leadership,” he said.

“Tom has been a steadfast and loyal colleague to so many of us – and we will be forever grateful for his wise advice, generosity, humour and decency.”