Teaching unions on Friday night demanded the closure of every school in the country after Gavin Williamson caved in to pressure to shut all primaries in London.
The Education Secretary was forced into a U-turn after councils threatened legal action over his decision to keep some schools in the capital open.
The move raises the prospect that pupils in other areas could also be kept at home, as a leading union insisted that "what is right for London is right for the rest of the country".
Dr Mary Bousted, the joint general secretary of the National Education Union, said the Government had corrected "an obviously nonsensical position", adding that ministers must "do their duty" by closing all primary and secondary schools to contain the virus.
It left the Government's policy on school reopenings in chaos just two days after Mr Williamson had resisted pressure from Cabinet colleagues to close schools on a region-by-region basis.
The development comes after Government scientific advisers warned that the spread of the new strain of coronavirus was unlikely to be halted if schools reopened, while an Imperial College study published on Friday said it may not be possible to "control transmission" if children go back to classes as planned.
There were fresh warnings on Friday night that the closure of schools to all but vulnerable children and the children of key workers will prove disastrous for students' education, with new questions about whether exams will go ahead as planned later in the year.
The Government has attempted to resist calls to close schools in recent weeks after the impact of doing so during the first lockdown was revealed. Analysis by the Education Endowment Foundation (EEF) charity revealed the decision had wiped out close to 10 years of progress in narrowing the attainment gap in England.
Meanwhile, scientists are divided on the impact of closing schools. Professor Tim Spector, the lead scientist on the ZOE Covid Symptom Study app, said children had been affected "the least of all age groups" despite rising cases, adding: "So if you want actions based on science,closing schools is a bad idea."
Labour council leaders in London gloated after forcing Mr Williamson into his latest U-turn. Danny Thorpe, the leader of Greenwich Council, said he was "absolutely delighted" that the Education Secretary had "finally climbed down".
Mr Williamson said the list of local authorities required to keep schools closed was being kept "under review", suggesting pupils' return could be further delayed.
The Government's current policy is to keep primary schools closed in some Tier 4 areas in the South-East, while secondary school pupils in years 11 and 13 will return on January 11 and others on January 18.
Several London districts with high coronavirus rates had been missed off the Government’s list of 50 "Covid hotspots" where primary schools were forced to close to most pupils for the next two weeks.
Eight council leaders in London had signalled that they could mount a legal challenge in response to Mr Williamson's original plan, calling the proposal "unlawful on a number of grounds".
The Education Secretary said expanding school closures had been a "last resort and a temporary solution", with primary schools in the capital now being encouraged to teach most of their pupils online.
But Dr Bousted said: "The question has to be asked: why are education ministers so inadequate and inept? Who is advising them?
"And what is right for London is right for the rest of the country. With the highest level of Covid-19 infection and hospitals buckling under the tsunami of very ill patients, it is time for ministers to do their duty – to protect the NHS by following Sage advice and close all primary and secondary schools to reduce the 'R' rate below one."
Research from Imperial College into the new "mutant" Covid-19 variant found it was directly affecting a greater proportion of those aged under 20. Axel Gandy, the chairman in statistics at Imperial College, said infections of the new variant would probably have tripled in two to three weeks under November's lockdown conditions.
"Overall, we've been able to determine that the new variant increases the reproduction number, so that's the number of people infected on average per infected person in the future, by about 0.4 to 0.7," he said. "That doesn’t sound like much, but the difference is quite extreme."
The Department for Education has said it will review the decision on school closures in the hotspot areas by January 18, but Boris Johnson has suggested this could be pushed back if coronavirus cases surge.
The decision to shut primary schools across London is the latest in a series of U-turns from Mr Williamson, including on exam results and face coverings in schools. It came after the eight London council leaders wrote to him to say they were "struggling to understand the rationale" behind a move that ignored "the interconnectedness of our city".
They said they had received legal advice that omitting some authorities from the list of areas told to take teaching online "is unlawful on a number of grounds and can be challenged in court".
The leaders of the Labour-run boroughs of Islington, Camden, Hackney, Lambeth, Lewisham, Greenwich, Haringey and Harrow all signed the letter, and Mr Thorpe said: "This is a decision that vindicates our safety-first approach we took at the end of the last term in the best interests of Greenwich. Faced with an exponential growth in Covid cases, we were clear immediate action was required.
"There remain huge questions to answer about how they ever came to this decision in the first place, and we will continue to push for those answers."
Kate Green, Labour's shadow education secretary, said: "This is yet another Government U-turn, creating chaos for parents just two days before the start of term. Gavin Williamson's incompetent handling of the return of schools and colleges is creating huge stress for parents, pupils, and school and college staff and damaging children’s education."
Ms Green called on Mr Williamson to "clarify" his position on schools in Tier 4 and set out the criteria for reopening.
It comes amid suggestions that the Government is considering making masks compulsory in secondary school classrooms. Schools Week reported that Department for Education officials had told a briefing on Wednesday evening that it would act to ensure teachers and pupils in Year Seven and above wear face coverings in class settings.
Sage advised ministers to extend the use of masks to "settings where they are not currently mandated, such as education, workplaces, and crowded outdoor spaces". The advisers also recommended "specifying higher performance face coverings and masks".