Headteachers have warned that staff shortages in the new term caused by teachers isolating because of positive lateral flow tests will be “challenging” for some schools and could lead to more pupils learning online.

Caroline Derbyshire, executive head at Saffron Walden County High School in Essex, and leader of Saffron Academy Trust, told the PA news agency: “We know that (staff shortages) will be a factor and there will be schools in particular parts of the country where rates have been extremely high where staffing will be difficult.

“But this sort of mass of supply teachers that are supposed to be there – that’s not happened, has it, so if we have got shortages it’ll be colleagues who are in school who’ll be doing most of the covering.”

I don't think anyone's looking forward to it at all

She said the idea of merging classes, as suggested by Education Secretary Nadhim Zahawi in the event of shortages, had already been carried out by schools “all term last term”, but it was “not a long-term solution”.

She said staff shortages would “absolutely” make remote learning more likely, adding: “If you hit a certain point with staff absences in a big school you’re talking about maybe 10 members of staff being off.

“You’ve suddenly got the inability to run a year group – that’s when you start having either year groups or whole parts of schools having to go online, so that’s when you’re going to have that mixed economy of some students being in school and some at home.”

She said this would be “a feature of this half term that we will have to manage, I don’t think anyone’s looking forward to it at all”.

Mr Zahawi outlined new Covid measures for schools on Sunday, saying he wanted to offer “reassurance” before the start of term.

Masks have been reintroduced in secondary classrooms, while all secondaries were asked to provide on-site testing for students ahead of their return to the classroom, and an additional 7,000 air cleaning units will be provided to schools, colleges and early years settings to improve ventilation in teaching spaces.

Mr Zahawi told Sky News on Monday that the “priority is to keep schools open”, and the Department for Education has suggested schools merge classes to keep face-to-face teaching in place.

Geoff Barton, general secretary of the Association of School and College Leaders, told PA that school bosses had responded to the reintroduction of face coverings for an initial two-week period with a “kind of weary, pragmatic acceptance that if that’s what we need to do to try to reduce transmission then that’s what we shall do”.

He added: “I think most people will hope that that’s a price worth paying to keep more young people in school, but ultimately that will come down to whether we’ve got enough staff when term starts tomorrow.”

Mr Barton said staff would have taken lateral flow tests over the weekend so there would be some waiting for PCR confirmation who would not be able to deliver face-to-face teaching.

“It’s hard to imagine that if the NHS is being affected, that retail is being affected, if sporting fixtures are being affected, it’s hard to see why you wouldn’t in schools and colleges have the same issues around staff shortages,” he said.

“But the difficulty is… heads will be in a position of, tomorrow, particularly secondary heads… they will first of all be trying to get the lateral flow test systems in place logistically so that all the young people are being tested, and at the same time it might be that they get a phone call at 8 from their curriculum deputy, saying, ‘actually, we’ve got 10 members of staff off today and the supply agency say they haven’t got enough people’.”

He said that Tuesday, when many pupils return, would “prove challenging” for some schools but “you just can’t predict where they might be or what it might look like”.

Paul Whiteman, general secretary of school leaders’ union NAHT, said schools were “taking the additional measures announced over the weekend in their stride” through arranging testing for pupils and informing parents and carers about the new rules on face coverings.

“They are hoping the extra measures will be enough to minimise disruption to education this term, but only the next few weeks will show how effective they really are,” he said.

“The biggest concern is staffing. Teachers and school staff will be testing and reporting their results at the start of this week and only then will school leaders know who they have available and be able to properly plan.

“School leaders will be doing everything possible to ensure a smooth return and a successful term for their students, but depending on how infection rates progress, it could be another stressful time.”

Councillor Phelim Mac Cafferty, leader of Brighton & Hove City Council, posted an open letter to Mr Zahawi on Twitter which said it would be “yet another school term which we fear will be filled with illness and disruption, as we try to keep our children’s education going during this new wave of the pandemic”.

He said the Department of Education’s announcement of 7,000 air cleaning units for schools, colleges and early years settings on Sunday, “while welcome, falls far short of the adequate number which are required, and will still leave most schools without”.

He added that the council would like face coverings recommended for older primary pupils too, while close contacts should be “required to isolate until they can show a negative PCR test”.

“The educational disruption this will cause will be less than that caused by allowing this highly transmissible variant to take hold in our school communities,” he said.