The Prime Minister has wished the Cabinet Secretary a “speedy recovery” as he takes time off from leading the Civil Service.

The Cabinet Office this week confirmed that Simon Case had stepped back from his role due to a “private medical matter”.

Updating ministers on Mr Case’s health-related absence during Tuesday’s Cabinet meeting, Prime Minister Rishi Sunak said the Cabinet Secretary was “taking a short period of leave”.

“The Prime Minister said the Cabinet Secretary was due to return in the coming weeks and that he knew colleagues would join him in wishing for a speedy recovery,” No 10 said in a readout of the meeting.

Downing Street said his duties would be “split out” and covered by a number of permanent secretaries and director generals while he is away.

The Prime Minister’s official spokesman said he would not “get into the detail of all aspects of” who would cover which responsibilities but said the director general of the Cabinet Secretariat took notes during Tuesday’s Cabinet session.

Mr Case’s absence comes after indiscreet WhatsApp messages during the pandemic were released by the UK Covid-19 Inquiry.

He had been expected to give evidence to the Covid inquiry in the coming weeks, after WhatsApp messages disclosed some of his private thoughts about Boris Johnson’s Conservative administration during the pandemic.

The head of the Civil Service said the Government was looking like a “terrible, tragic joke”, while Mr Johnson’s wife Carrie was “the real person in charge”.

Mr Case, who was made Cabinet Secretary in September 2020, having been permanent secretary in Number 10 before then, wrote that he was “not sure I can cope” amid apparent frustration at how the pandemic was being handled.

The Cabinet Secretary was embroiled in the partygate row and had to step back from the investigation into lockdown-breaking parties, which ultimately fell to Sue Gray to lead, because of his own involvement.

He was pictured at the Cabinet Room birthday party for which Mr Johnson and Mr Sunak were fined.

A spokesman for the UK Covid-19 Inquiry said: “Further to press reports about the Cabinet Secretary over the weekend, the inquiry legal team can confirm it has been contacted by Government lawyers.

“We will update core participants as soon as possible.”

Mr Case’s central role during the Johnson premiership also saw him drawn into the rows surrounding Richard Sharp’s appointment as BBC chairman.

Separately, he admitted he had an “informal conversation” about potential roles at a royal charity for Mrs Johnson after a prompt from No 10.

Before entering Mr Johnson’s Downing Street operation, the 44-year-old had previously served as private secretary to the Prince of Wales while he was Duke of Cambridge.

He also worked in No 10 during David Cameron’s tenure, including a stint working as his private secretary.