No. 10 said sorry after it emerged two gatherings took place on the night before Prince Philip's funeral in April last year, during which the Queen was pictured sitting alone due to Covid restrictions.
Staff reportedly drank to excess and danced, with one allegedly sent to a Co-op to fill a suitcase with bottles of wine.
In a separate incident, the former director general of the UK Government’s Covid taskforce also apologised for having leaving drinks in her office during lockdown.
Kate Josephs said she was “truly sorry” for the gathering, which took place in the Cabinet Office to mark her exiting the Civil Service on December 17, 2020.
The revelations pile further pressure on the Prime Minister, who is facing mounting anger and internal calls to resign, including from Scottish Tory leader Douglas Ross.
A Tory source told The Scotsman that news of the two gatherings on the eve of Prince Philip's funeral had led to more MPs submitting letters of no confidence in Mr Johnson.
The Daily Telegraph, which broke the news of the latest parties, reported as many as 30 letters had been submitted by Friday. A total of 54 are needed to trigger a vote.
A spokesman for the Prime Minister confirmed No. 10 had said sorry to the Palace.
He said: “It is deeply regrettable that this took place at a time of national mourning and No. 10 has apologised to the Palace.
“You heard from the PM this week, he’s recognised No. 10 should be held to the highest standards, and take responsibility for things we did not get right.”
The day after the parties on April 16 last year, the Queen attended her husband Philip’s funeral wearing a face mask and socially distanced from her family at Windsor Castle, in line with Covid restrictions.
The Prime Minister’s spokesman said Mr Johnson was at his country residence and had not been invited to the events.
Asked why No. 10 had apologised rather than Mr Johnson himself, his spokesman told reporters: "Well, again, the Prime Minister said earlier misjudgements have been made and it's right people apologise, as the PM did earlier this week."
It is understood the apology was delivered via a telephone call through official channels.
Labour leader Sir Keir Starmer said Mr Johnson should also be offering the Queen his resignation.
He said: “The Conservatives have let Britain down. An apology isn’t the only thing the Prime Minister should be offering the palace today.
“Boris Johnson should do the decent thing and resign.”
The SNP branded Mr Johnson “unfit for office”.
One of the events in April was a leaving do held for the Prime Minister’s former director of communications James Slack, who is now deputy editor-in-chief of The Sun newspaper.
In an emailed statement issued by The Sun’s publisher, News UK, he said he took “full responsibility” and was “deeply sorry”.
Mr Slack said: “This event should not have happened at the time that it did.”
Ms Josephs, who is now the chief executive of Sheffield City Council, later also apologised "unreservedly".
Dozens of officials from the Cabinet Office’s Covid-19 taskforce were reported to have attended her leaving event while the country was in lockdown.
On that same day, the Government’s official Twitter feed replied to a query asking if employers could hold Christmas parties at the end of the working day.
It explained that "although there are exemptions for work purposes, you must not have a work Christmas lunch or party, where that is a primarily social activity and is not otherwise permitted by the rules in your tier".
In a statement posted on Twitter, Ms Josephs said: “On the evening of 17 December, I gathered with colleagues that were at work that day, with drinks, in our office in the Cabinet Office, to mark my leaving the Civil Service.
“I am truly sorry that I did this and for the anger that people will feel as a result. Sheffield has suffered greatly during this pandemic and I apologise unreservedly.
“The specific facts of this event will be considered in the context of the Cabinet Office investigation. I did not attend any events at 10 Downing St.
“I am grateful for the ongoing support of colleagues and partners and need now to ask that people allow the Cabinet Office to complete its investigation.
“I will not be able to respond to any further questions until the Cabinet Office investigation is complete.”
It brings the total number of parties or gatherings alleged to have happened across Whitehall during restrictions to 15.
On Wednesday, the Prime Minister apologised for attending a “bring your own booze” party in the Downing Street garden in May 2020, during the first coronavirus lockdown, but insisted he believed it was a work event and could “technically” have been within the rules.
The gatherings are being probed by senior civil servant Sue Gray, who is due to report back at the end of next week.
The Times reported that her inquiry is expected to find no evidence of criminality, but the investigation could censure Mr Johnson and criticise the culture in Downing Street.
Scottish Tory MSPs have backed Mr Ross’s call for the Prime Minister to resign, with widespread anger over the revelations within the group.
But Conservative MSP Craig Hoy denied the Tories are now “two parties”.
He told the BBC: “We’re not two parties at all.”
Mr Hoy continued: “There’s absolute unanimity that we believe in Scotland remaining in the UK.
“We want to take the fight to the SNP, we want to hold Nicola Sturgeon to account for her failures in office.”