Schools in England are “bleeding out” with thousands of teachers having to isolate under a bubble system that is harming the most vulnerable children, ministers have been warned.

Headteachers are growing increasingly exasperated about a lack of clarity from the government about how to deal with Covid outbreaks among pupils, with only two weeks until most schools in England break up for summer.

Gerard Jones, the director of children and young people at Oldham council, said the town was struggling to keep schools open with 400 staff isolating along with more than 6,400 children – about 15% of the whole school population.

“What we’re getting from the government is ‘be patient’ and the Department for Education have just refused to say very much about it at all. Meanwhile we’re bleeding out here,” he said.

Jones said the much-criticised policy of sending home dozens of pupils if one tested positive was increasing the risk of harm to vulnerable children at home. “What we saw during the last lockdown was a lot of children come to harm because they were not being seen at school, so we always worry about that.”

The education secretary, Gavin Williamson, said last week he wanted the bubble system scrapped as soon as possible, but the government has not yet announced how it will be replaced.

Ministers are said to be considering a “test and release” system, which would allow pupils or staff who have been in contact with an infected person to remain at school as long as they produce a daily negative test.

A sharp rise in school Covid outbreaks meant that 330,000 pupils in England were isolating at home the week before last, with that figure expected to rise in the final days of term.

Prof Adam Finn, a paediatrics expert and member of the Joint Committee on Vaccination and Immunisation, said the greatest threat to children from Covid was “primarily through disruption to their development and education”.

He said: “It’s clear not just in schools but in society more generally that because of the rapid rise in cases and the number of contacts, a lot of areas of activity have been paralysed by the need to isolate.

“So there’s an emerging dilemma there that either you accept that kind of paralysis or you relax the rules. At some point, whether it’s schools or workplaces, we’re going to have a kind of de facto lockdown, simply because so many people are being asked to self-isolate.”

Jones, who is responsible for about 35,000 children in Oldham’s 72 schools, said the bubble system was putting younger children’s health at risk because it meant that those isolating may miss out on vaccinations for measles, mumps and rubella.

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“We need a new plan for daily testing and a reformed approach to how we handle Covid in schools and we need these not in three months but now,” he said. “This is not just an issue Oldham is facing but is being seen across Greater Manchester with thousands of pupils affected. Northern kids are at risk of being left behind – when exams do go ahead children from wealthier boroughs will have had far more schooling.

“If this was happening in Westminster, there would be action – if this government is serious about levelling up, they need to put their hands in their pockets and give us the resources to help these children now.”

A Department for Education spokesperson said: “We are grateful to everyone who works in education for their tireless work over the course of the pandemic – and for following safety measures to protect public health while maintaining high-quality teaching for pupils.

“We recognise the disruption that a minority of schools and colleges continue to face, which is why we are working across government to relax restrictions and provide clarity on the new approach in line with the wider move to step 4 of the roadmap.”

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