Boris Johnson’s brother has dramatically quit the government – and parliament – in an apparent protest at the prime minister’s leadership.

Jo Johnson, a higher education minister, said it was impossible to reconcile “family loyalty and the national interest”, adding: “It’s an unresolvable tension and time for others to take on my roles as MP and minister #overandout.”

It is only six weeks since the younger Johnson faced fierce criticism for returning to serve his brother – despite resigning for the first time late last year, to campaign for a Final Say referendum on Brexit.

It leaves the prime minister with the painful task of trying to explain why even his own sibling has lost faith in his handling of the Brexit crisis, as the criticism of Tory MPs grows.

In a bombshell tweet, Jo Johnson wrote: “In recent weeks I’ve been torn between family loyalty and the national interest,” – before going on to describe it as “an unresolvable tension”.

It is understood that Jo Johnson informed the prime minister of his plan to resign in a phone call on Wednesday evening.

One Westminster observer immediately summed up his decision to walk out as sending the message: “I’m resigning to spend less time with my family.”

Others pointed back to an interview Boris Johnson gave, a few years ago, in which he insisted he and his brother would never suffer a family schism like David and Ed Miliband.

“We don’t do things that way, that’s a very left-wing thing,” the older Johnson said.

“Only a socialist could do that to his brother, only a socialist could regard familial ties as being so trivial as to shaft his own brother.”

It appeared the final straw for Jo Johnson was his brother’s decision to “purge” 21 moderate Conservatives from the party, for their rebellion to block a no-deal Brexit.

Among the exiled MPs were colleagues, such as Justine Greening, with whom he had – before the summer – been working to try to avert a crash out from the EU.

One of the 21, former defence minister Guto Bebb, told The Independent that the resignation was “absolutely devastating to the credibility of Boris Johnson”.

“In effect, Jo is saying he has wrestled with the choice between loyalty to his brother or loyalty to the national interest and has concluded that loyalty to the national interest has to come first,” said Mr Bebb.

“This is Jo Johnson – who is a decent, honourable person – saying quite categorically that his brother is not acting in the national interest.”

Mr Bebb said he expected opposition parties to exploit the schism between the brothers in the same way that Conservatives did the rivalry between the Milibands, in a way which would be “very damaging” to the Tory cause in the expected election.

But another former minister told The Independent: “It’s not the same. Ed Miliband was challenging his brother. Jo is vacating the scene. His decision to leave parliament makes clear he is not doing this to damage his brother.”

And former justice secretary David Gauke, who had the whip removed after rebelling on Tuesday, said: “Lots of MPs have had to wrestle with conflicting loyalties in recent weeks. None more so than Jo. This is a big loss to parliament, the government and the Conservative Party.”

Angela Rayner MP, Labour’s shadow education secretary, said: “Boris Johnson poses such a threat that even his own brother doesn’t trust him.”

The resignation caps a horror 24 hours for the new prime minister, who has yet to win a Commons vote – while suffering multiple defeats at the hands of rebel Tories.

The Commons refused to grant Mr Johnson a snap general election, less than two hours after passing a bill designed to block a no-deal Brexit on 31 October.

An election could yet be granted for his chosen date of 15 October if the bill becomes law by Tuesday, but Jeremy Corbyn is facing a growing Labour revolt to delay it further.

When he first resigned, in November 2018, Jo Johnson branded Theresa May’s negotiations as a “failure of British statecraft on a scale unseen since the Suez crisis”.

Warning Britain stood “on the brink of the greatest crisis since the Second World War”, Mr Johnson added: “The democratic thing to do is to give the public the final say.”

A No 10 spokesman said: “The prime minister would like to thank Jo Johnson for his service.

“He has been a brilliant, talented minister and a fantastic MP. The PM, as both a politician and brother, understands this will not have been an easy matter for Jo.”