The Prime Minister wished the Cabinet Secretary a “speedy recovery” as he takes leave from the leadership of the Civil Service.
The Cabinet Office this week confirmed that Simon Case had stepped down from his role due to a “private medical matter”.
Informing ministers of Mr Case's health-related absence during Tuesday's cabinet meeting, Prime Minister Rishi Sunak said the cabinet secretary had “taken a short leave”.
“The Prime Minister said the Cabinet Secretary was due back in the coming weeks and he knew his colleagues would join him in wishing him a speedy recovery,” No 10 said in a reading of the meeting.
Downing Street said his duties would be “separated” and filled by a number of permanent secretaries and directors-general while he is away.
The Prime Minister's official spokesman said he would not “go into detail on all aspects” of who would cover which responsibilities, but said the director-general of the Cabinet Secretariat had taken notes during Tuesday's Cabinet meeting.
Mr Case's absence comes after the UK's Covid-19 inquiry released undisclosed WhatsApp messages during the pandemic.
He was expected to give evidence to the Covid inquiry in the coming weeks after WhatsApp messages revealed some of his private thoughts about Boris Johnson's Tory administration during the pandemic.
The head of the Civil Service said the government looked like a “terrible, tragic joke” while Johnson's wife Carrie was “the real person in charge”.
Mr Case, who became Cabinet Secretary in September 2020, having previously served as permanent secretary at Number 10, wrote that he was “not sure I can cope” amid apparent frustration at the way the pandemic has been handled.
The cabinet secretary was embroiled in the partygate controversy and had to stand down from the inquiry into lockdown-breaking parties, which eventually fell to Sue Gray to lead, because of his own involvement.
He was photographed at the Cabinet Room birthday party for which Messrs Johnson and Sunak were fined.
Mr Case's central role during Johnson's premiership also saw him embroiled in controversy surrounding the appointment of Richard Sharpe as chairman of the BBC.
Separately, he admitted he had an “informal chat” about possible roles at a royal charity for Mrs Johnson at No 10's prompting.
Before joining Johnson's Downing Street business, the 44-year-old previously served as private secretary to the Prince of Wales while he was the Duke of Cambridge.
He also worked at No 10 during David Cameron's tenure, including a stint as his private secretary.