Civil service chief Simon Case has stepped back from his role due to a “private medical matter”.
Mr Case, whose time in the job has seen him involved in a series of controversies, is expected to be absent for “a few weeks”.
The Cabinet Office confirmed Mr Case’s absence, which comes just days after indiscreet WhatsApp messages during the pandemic were released by the UK Covid-19 Inquiry.
Politico, which first reported his absence, said Rishi Sunak would brief the Cabinet about the situation, with elements of Mr Case’s role being filled by a number of top officials while he is off, rather than anyone standing in as Cabinet Secretary.
A Cabinet Office spokesman said: “The Cabinet Secretary is taking a short period of leave because of a private medical matter and is due to return to work in a few weeks.”
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 government 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 in Government.
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.
Mr Case’s central role during the Johnson administration also saw him drawn into the rows surrounding Richard Sharp’s appointment as BBC chairman.
He also admitted he had an “informal conversation” about potential roles at a royal charity for Mrs Johnson after a prompt from No 10.