Prime minister Boris Johnson is set to close all schools for weeks, it has been reported, as a chaotic start to the new term saw primaries shut across England due to staff safety concerns.

According to the Financial Times, the Cabinet agreed today to partial school closures until possibly February half-term as part of a national lockdown planned in response to a surge in Covid-19 infections and a new variant in the virus. Prime minister Boris Johnson will address the nation at 8pm.

It comes amid reports of widespread closures of primary schools across England this week after the government’s botched back-to-school announcements.

All primaries apart from those in certain “hotspot” areas were asked to resume face-to-face teaching for all pupils this week. However some primaries had to move to remote learning after staff invoked their right not to work in an unsafe environment.

Under section 44 of the employment rights act 1996, employees have the right “not to be subjected to any detriment” if they leave or refuse to return to work because they believe it is dangerous.

Teaching and support staff unions urged members over the weekend to use those protections if they felt that returning to work would make them unsafe.

In Wiltshire, the Wellington Lions and Wellington Eagles academies in Tidworth were unable to open today due to “insufficient staffing levels”, while Even Swindon Primary School said it could not open to pupils after a “significant number of teaching staff” invoked their rights.

In Wigan, St Mark’s primary school closed to all pupils except those in year six, vulnerable pupils and the children of key workers. Headteacher Kayleigh Ferguson wrote on Facebook that the decision of some staff to invoke their rights meant there was a “lack of staffing capacity”.

And in York, Copmanthorpe Primary School told parents it would be open only to vulnerable pupils and the children of critical workers from tomorrow, citing “a majority of staff” invoking section 44 of the act.

It is not known how many staff have issued so-called section 44 letters to their schools, but the National Education Union reported this morning that around 6,000 primary schools had received them.

Closures outside the hotspot zones were more widespread in some areas than others. In Wolverhampton, 35 of 48 schools that had declared their intention to open or close on Monday had decided to teach children remotely, according to the Express and Star newspaper.

But many primary schools had an inset day today, meaning the extent of partial closures may not be known until later in the week.

Paul Whiteman, general secretary of the NAHT school leaders’ union, said it was “very hard to tell how many school buildings have been open today”.

“But you can bet that where possible, school leaders will have done everything they can to offer the maximum provision that their circumstances allow. Some schools in tier four areas will be open for vulnerable pupils and key worker families and will be providing remote learning for others, yet in other areas also in tier four, all pupils will be admitted. That’s a confusing picture for school leaders and families alike.”

It comes as leaders anxiously await news of new lockdown restrictions, due to be announced by the prime minister in an 8pm televised briefing. A new national lockdown in Scotland, announced earlier today, will see schools partially closed until February.

Johnson has come under growing pressure to keep the majority of pupils away from schools amid fears about the spread of the virus. That pressure initially came from unions, which called over the weekend for primary schools to move to remote learning for all but the most vulnerable pupils and children of key workers for at least two weeks.

However, calls for closures have also come from prominent politicians, including former health secretary and health committee chair Jeremy Hunt.

Labour initially stopped short of calling for further closures yesterday, but leader Sir Keir Starmer said today that schools would need to be “part of the national restrictions that come into place as soon as possible”.

At least two dozen councils in areas outside the government’s list of hotspots have now said they will back school leaders that take the decision to partially close.

Brighton and Hove and Birmingham councils were among the first to do so over the weekend, but others, including Wiltshire, Bristol, Manchester, Rochdale, Cumbria, Northumberland, Newcastle, Birmingham and Walsall have now followed suit.

Kent, which currently has nine of its 13 districts on the hotspot lists, has urged the government to call for the closure of primary schools in the remaining four areas, while Essex council, which has 11 areas on the list, has called for “urgent clarity” over what should happen in the remaining three.

The decision to partially close schools sits with school leaders, but the government has powers under emergency coronavirus legislation to compel individual or groups of schools to open or shut to some or all pupils.

Johnson has repeatedly refused to say when asked yesterday whether ministers would take action against councils backing schools to close, as they did with Greenwich before Christmas.

Just yesterday, the PM claimed schools were “safe”.

It has also emerged that the Department for Education has sought and been granted an extension to the deadline to provide information to the NAHT and ASCL leadership unions under legal action launched last week.

The unions want to know more about the scientific advice the government is drawing on and arrangements for testing. The department had until 4pm today to respond, but Schools Week understands it has now been granted an extension until noon tomorrow.