Boris Johnson stepped in to protect Dominic Cummings on Sunday night in a move that caused alarm among some members of the Cabinet.
The Prime Minister made an unscheduled appearance at a Downing Street press conference in which he defended his chief adviser against accusations that he had breached lockdown rules, insisting that Mr Cummings had "acted responsibly and legally and with integrity".
Cabinet colleagues, however, voiced fears that the move risked "seriously undermining" the Government’s lockdown strategy.
Some even suggested the support for Mr Cummings could cost lives because the public would use it as justification for ignoring social distancing.
Meanwhile, Government scientific advisers said Mr Johnson had "trashed" the advice they had given him on how to build trust in the measures needed to keep coronavirus under control.
The Prime Minister said Mr Cummings had been following "instinct" when he drove his family from London to Durham to self-isolate at his parents' farm.
He said: "I've had extensive face-to-face conversations with Dominic Cummings and I concluded that, in travelling to find the right kind of childcare at the moment when both he and his wife were about to be incapacitated by coronavirus, and when he had no alternative, I think he followed the instincts of every father, and every parent. I do not mark him down for that."
However, it has led to questions about whether people should now follow their instincts rather than the rules.
On Sunday night, Robin Lees, a retired chemistry teacher, made a complaint to police in which he reported seeing Mr Cummings and his family on a day out in Barnard Castle on April 12.
Mr Lees told police in Durham he believed Mr Cummings had breached health protection regulations.
A Liberal Democrat councillor has also made a complaint to police in Durham, who were reported to be considering whether they need to take further action.
Grant Shapps, the Transport Secretary, appeared to confirm the family trip to Barnard Castle – on the 45th birthday of Mr Cummings' wife, Mary Wakefield – when he told the BBC's Andrew Marr that Mr Cummings was out of self-isolation by then.
Mr Johnson's appearance came after a day of drama during which Mr Cummings was besieged by journalists at his London home.
When he returned home, the chief adviser was heckled by neighbours from their windows as he walked down his street. One shouted: "People couldn't go to funerals. What have you got to say to that?"
A woman shouted: "My Mum's terrified. My Dad's had three shoulder operations and she won't let him go to the park, she won't even entertain me in her garden."
Another woman had scrawled graffiti on the street saying Mr Cummings was "hopefully going".
After two days of damaging revelations about Mr Cummings' actions, Mr Johnson risked not only his coronavirus strategy but also party unity with his decision not to sack him following a meeting in Downing Street.
The decision sparked anger at all levels of the party, and friends of the Prime Minister are also concerned that, by binding his own reputation so tightly to that of Mr Cummings, he risks being tainted by any further disclosures.
Senior Tory MPs publicly called for Mr Johnson to sack Mr Cummings, saying his position had become "untenable", while others expressed a similar message to party whips.
The Prime Minister's unscheduled appearance at the press conference failed to subdue a row that threatens to overshadow announcements this week on the next phase of the lockdown.
He failed to answer a host of questions from journalists, such as when he became aware of Mr Cummings' 520-mile round trip, whether he had sanctioned it, or whether he accepted that his adviser had broken lockdown a second time by driving 30 miles from Durham to Barnard Castle for a day out when such behaviour was forbidden.
One Cabinet source told The Telegraph: "The discussion among Cabinet ministers at the moment is that this will cost lives.
"People will look at this and decide that if Dom can ignore the rules so can they, and the consequence of that will be that people get infected who would have otherwise stayed at home. This has massively undermined the lockdown message."
Another senior Tory source said: "Boris has put his credibility and the Government's credibility on the line by sticking up for Dom.
"How can we tell people they must abide by the lockdown now? The lockdown is effectively over, because this makes it unenforceable."
Stephen Reicher, a member of the SPI-B committee that advises the Government on behavioural science, said: "In a few short minutes tonight, Boris Johnson has trashed all the advice we have given on how to build trust and secure adherence to the measures necessary to control Covid-19.”
Susan Michie and Robert West, both members of SPI-B, tweeted that they agreed.
Tory MPs shared messages on a WhatsApp group that had been sent to them by angry constituents demanding to know why they had been forced to miss funerals or other important events if the rules were open to interpretation.
Former Brexit minister Steve Baker said it was an "insult" to people who had diligently obeyed the lockdown rules and made huge personal sacrifices. Peter Bone said the "vast, vast majority" of Conservative MPs now wanted Mr Cummings out of Number 10.
Mr Johnson said he had decided to appear at the press conference because he was aware that people were asking: "Is this Government asking you, the people, the public to do one thing while senior people here in Government... have been basically flouting those rules and endangering lives?"
He said the answer was: "I believe that in every respect, he [Mr Cummings] has acted responsibly and legally and with integrity, and with the overwhelming aim of stopping the spread of the virus and saving lives."
Sir Keir Starmer, the Labour leader, said: "This was a test of the Prime Minister and he has failed it. The public will be forgiven for thinking there is one rule for the Prime Minister's closest adviser and another for the British people.
"The Prime Minister's actions have undermined confidence in his own public health message at this crucial time. Millions were watching for answers, and they got nothing."
He said the Cabinet Secretary, Sir Mark Sedwill, should launch an "urgent inquiry" into the affair.