The prime minister received a test despite having no symptoms – something denied to most people, although a trial is underway in Liverpool and in some workplaces.
Downing Street denied any “special treatment”, saying a workplace trial of asymptomatic testing had begun in No 10 two weeks ago.
The 14-day shutaway will impose a big cost on Mr Johnson, who will be barred from the Commons for next week’s spending review and the setting out of plans to escape the lockdown on 2 December.
Ministers have spent weeks trying to agree a cut to the self-isolation period, but Dominic Cummings’ bid to slash it to just 7 days is thought to have been blocked by Chris Whitty.
Mr Johnson’s spokesman said his isolation would have “no bearing” on the timing of any changes – which meant he had to shut himself way for two weeks
“The rules are the same for everybody in every part of the country and the prime minister is following them the same as every other member of the public,” he said.
The spokesman confirmed an agreement had been reached for him to take part in prime minister’s questions – on a screen from No 10 – on Wednesday.
No 10 also all-but admitted that it intends to scrap the commitment to spending 0.7 per cent of national income on overseas aid, in next week’s spending statement.
“It is legitimate to consider where savings can be made when public finances are under huge strain,” the spokesman said.
A get-out clause in the Act which made 0.7 per cent a legal commitment – in circumstances such as a severe economic downturn – will be used to make the controversial U-turn.
On Brexit, it it now expected that any deal will not be struck until next week at the earliest – despite the EU’s attempt to impose a deadline of Thursday this week.
The government was still “working hard to get a deal, but it is far from certain if that will prove possible,” the spokesman said.
Mr Johnson was told to isolate after hosting a group of Tory MPs at No 10 last week, one of whom then tested positive – drawing criticism of lax precautions at the centre of power.
He received a new lateral flow test, “on a precautionary basis”, despite fears they are less reliable than the standard lab tests.
