Secondary pupils could go on to a classroom rota under a “circuit-breaker” national lockdown.
Unions have warned the Government could trigger it’s “Plan B” option to keep schools open by teaching older children remotely for two week spells – with the rest of the time at their desks.
Geoff Barton, chief of the Association of School and College Leaders, said the Government had a four-tier plan.
He said: “The first is to keep everyone in school, the second is to leave in all primary children but move to a rota for secondary, the third is for all secondary to remain at home and the fourth is to go back to a total shutdown.
“I think the second is the more likely scenario in any new lockdown.”
Fears over children’s mental health are growing.
Charity Place2Be said 9,000 staff had applied for its course in supporting pupils under stress.
Clinical director Dr Niki Cooper said: “Children tend to manage best when adults are coping. It’s crucial teachers support each other.”
A teaching union leader has also warned schools are struggling to cope with a lack of Covid-19 tests for pupils and staff as the situation is becoming "increasingly out of control".
Dr Patrick Roach, general secretary of the NASUWT teaching union, has called on the Government to prioritise the education sector for the allocation of tests in light of widespread challenges.
The Association of School and College Leaders (ASCL) said it has received 264 responses from schools and colleges in recent days where leaders have said they have symptomatic staff and/or pupils who were struggling to access tests.
Education Secretary Gavin Williamson said each school was given 10 home-testing kits at the start of term and schools can now order more from the NHS directly.
Rob Halfon, chairman of the Commons Education Committee, asked if he could guarantee pupils and teachers who need local Covid-19 tests would be able to get them within 48 hours in the event of outbreaks.
Mr Williamson replied: "Schools are, I think, the only organisation that actually has a set of testing kits that have been sent to them directly in order to be able to ensure that if they are in a situation where someone isn't in a position to be able to get a test, then they actually have testing kits on site."
Schools have been hit with Covid-19 cases since it became compulsory for pupils to return.
Some have closed their doors days after reopening while others have told whole year groups and classes to self-isolate for two weeks following confirmed cases.
In a letter to schools minister Nick Gibb, Dr Roach said: "Schools appear to be seeking to do their utmost to carry on.
"However, we have reports that schools are unable to cope with a situation that is becoming increasingly out of control."