Opposition MPs claim Dominic Cummings played a behind-the-scenes role in ousting Sir Mark Sedwill from his position at the top of the Civil Service.

Sir Mark, the most powerful official in Government, announced on Sunday he had agreed to pack his bags and stand down from his role as both Cabinet Secretary and the UK’s national security adviser.

It comes after multiple reports suggested Mr Cummings, the Prime Minister’s chief aide, had encouraged the PM to give the former diplomat the boot.

In his letter to Boris Johnson announcing his resignation, Sir Mark inferred that the PM had wanted him to go, writing: “We have agreed that I will stand down and leave government service at the end of September.”

Sir Mark’s removal was seen as a win for Mr Cummings who, according to The Times, is said to have told a meeting of political aides this week that a “hard rain is going to fall” after explaining he felt Whitehall’s shortcomings had been uncovered during the coronavirus crisis.

Sir Ed Davey, acting leader of the Liberal Democrats, said Mr Johnson had given his de facto chief of staff what he wanted in forcing the Cabinet Secretary out.

Why have Dominic Cummings and Boris Johnson decided that now is the time for a hard rain to fall on our loyal civil servants?

“Boris Johnson is clearly ready to grant Cummings his every wish when it comes to politicising the Civil Service and sweeping out those who may try to hold his Government to account,” said the former energy secretary.

Labour’s shadow housing secretary Thangam Debbonaire questioned the timing of the announcement and insinuated Mr Cummings had worked with the PM on the decision.

Speaking to BBC Radio 4’s Westminster Hour, she said: “Why should this happen now?

“Why have Dominic Cummings and Boris Johnson decided that now is the time for a hard rain to fall on our loyal civil servants?

“We are in the middle of a national, an international crisis of massive proportions.”

It is not the first time Mr Cummings, recently in the firing line after it was revealed he drove 260 miles during the lockdown when travel was still banned, is thought to have intervened in the firing of a senior official.

He infuriated ex-chancellor Sajid Javid by sacking one of his then aides, Sonia Khan, and having her escorted from Downing Street by police after having apparently blaming her for the leaking of a Treasury report on the risks from Brexit.

The FDA, the civil servants’ union, claimed Sir Mark had been “cowardly” briefed against.

General secretary Dave Penman said: “No.10, or those around it, has sought to undermine Sir Mark and the leadership of the civil service, with a series of anonymous briefings against him over many months.”

The PM’s decision to promote David Frost, his Europe adviser, to national security adviser (NSA) has also raised eyebrows.

It is the first time the job has gone to a political appointee, with Mr Frost to continue to oversee the trade negotiations with Brussels.

I will of course remain chief negotiator for the EU talks and these will remain my top single priority until those negotiations have concluded, one way or another

He will begin shadowing Sir Mark in the NSA role in August to carry out a handover phase with his outgoing predecessor.

Mr Frost said: “I will of course remain chief negotiator for the EU talks and these will remain my top single priority until those negotiations have concluded, one way or another.”

Lib Dem Brexit spokesman Alistair Carmichael said allowing the experienced diplomat to hold dual roles demonstrated “a lack of seriousness about EU trade negotiations” and that it pointed to “a further politicisation of the civil service” under Mr Johnson.

As part of accepting to depart in September, Mr Johnson has nominated Sir Mark for a life peerage, and has also asked him to lead a new G7 panel on global economic security as the UK prepares to assume the presidency next year.

He will also receive a “departure package in line with the normal rules governing civil service pensions and compensation”, according to a Government spokeswoman.

Like Sir Mark, Mr Frost has also been nominated by the PM for a life peerage in the House of Lords.