Will Coombs (not his real name) has to test the blood of his 10-year-old son, Jamie, every two hours, even at night. Jamie has brittle diabetes, a rare form of type 1 diabetes that causes severe swings in his blood sugar levels. Before the pandemic he was hospitalised after catching a cold; on another occasion, with a stomach bug.

The family decided to home school their three children to keep Jamie safe from Covid. His hospital consultant supports the family’s decision. But the government is threatening them with fines or prosecution if the children do not return to class.

His parents are used to being cautious when even trivial viruses are circulating at school, because they can cause Jamie’s blood sugar to fluctuate dangerously. People with diabetes have been disproportionately affected by Covid, and are much more likely to develop serious complications.

“Education is important but health should be the priority,” says Coombs. “You cannot learn if you are seriously ill or worse as a result of catching Covid.” He believes the Department for Education’s stance on attendance at all costs is discriminatory.

The latest DfE data estimates 320,000 pupils were absent for Covid-related reasons in England on 3 February. With many of his children’s school friends on their second or third Covid infection and masks no longer compulsory, Coombs is adamant that he is right to teach his three children at home. The authorities disagree.

Jamie’s consultant wrote recently to his brother’s secondary school urging it to be “as supportive as possible” of the family’s decision to home school until all three children had been vaccinated and case rates were lower. But now, after advice from the DfE, the local authority has instructed the school not to send any work home to the family, and threatened them with fines or prosecution. The primary school that Jamie and his sister attend has made the same threats.

Coombs doesn’t blame the headteachers, or even the council. He blames the government. He says the secondary school head “understands where we are coming from” but is under pressure to lean on families like his. He says the head has been told by the DfE that shielding has finished and all pupils must now be back in school.

Coombs, who trained as a teacher, says: “Heads and teachers know the families and understand the issues and individual circumstances. Why can’t they be trusted to make a sensible decision on each case?”

The government is consulting on more prescriptive plans to boost attendance and end what it calls a postcode lottery of how schools manage absences. These sorts of Covid cases are a grey area for schools. The education secretary, Nadhim Zahawi, has confirmed in a letter to the Good Law Project that heads can exercise discretion over individual cases, but in practice schools say the very clear directive from the DfE is that all children must return to the classroom and they feel under pressure to deliver that. Parents who are home schooling because of Covid say schools are not giving them any work in case they are seen to support unauthorised absences.

In January the Centre for Social Justice, a rightwing thinktank, raised fears about so-called “ghost children”, with a report claiming that severe absence “has spread across our school system like wildfire”. It said that in autumn 2020 more than 700 state schools were missing an entire class-worth of children. Dame Rachel de Souza, the children’s commissioner in England, has vowed to track down missing children.

But families like the Coombses say theirs is a different story that needs to be heard. Their children are not vanishing, they are merely being protected by their families because they do not think there are enough mitigations in school to keep them safe. Many say, paradoxically, that the pressure from the DfE is forcing them to consider opting out of the system permanently.

April Booth, a co-founder of a parent campaign group, Safe Ed For All, will appear in court on 25 February for refusing to send her son, Casper, back to his secondary school in Portsmouth while cases remain high. She risks a fine of up to £2,500, which she cannot afford, or three months in prison.

She says: “I’m not an activist and I have been scared at times. I know so many people who have deregistered [their children from school] rather than face court, but my son wants to go back to school when things improve. The government is criminalising parents for trying to protect their children during a health crisis.”

Booth took Casper out of school in 2020 when his grandfather was hospitalised with Covid for four months and nearly died. Casper, now in year 8, hasn’t returned since. She describes the lack of mitigations to protect children and their vulnerable family members as “mind-boggling”.

“I’ll be happy to return him to school when community transmission is a lot lower, when far more children are wearing masks and ventilation has been looked at properly,” she says.

Casper’s school says attendance is mandatory and “the vast majority of parents have confidence” in what it is doing. A spokesperson said: “Missing school means students fall behind, which has serious consequences for their progression.”

Kim Wareham, from Bath, reluctantly deregistered her 10-year-old daughter, who has a learning disability and a rare genetic syndrome, from her special needs school last week after keeping her at home since numbers rose with Omicron.

Wareham says she deregistered because, without remote work being sent home for her daughter, she felt she had been shut out of the system. “We were learning about electricity and my daughter made a torch out of a cardboard tube and wired up the circuits. She was so proud of it and we sent a photo, but so far we’ve heard nothing back. That’s sad.”

“Having my daughter around all the time is wonderful,” she says. “But it is so important she mixes with peers who face similar life and learning issues. It feels really unfair that we’ve had to remove her.”

The head of a primary school in Kent, who asked not to be named, said: “We use a range of strategies to try to encourage parents to bring children in. The risk is that if you push them too hard they self-select to home educate and are never seen again in the education system.”

Geoff Barton, the general secretary of the Association of School and College Leaders, says cracking down on attendance will be a key part of the forthcoming schools white paper. “I’ve been saying you must be so careful not to demonise parents and make them feel they are the problem,” he says.

Gemma Moss, of University College London’s Institute of Education, led a research project looking at how schools have interacted with families during the pandemic. “The problem is the government isn’t trusting teachers and is ignoring the personal relationships they have with families. You can’t map all of this from the centre,” she says. “We looked at primary schools and they are deeply embedded in their communities. Headteachers would go and knock on doors if they hadn’t heard from a family and were worried about a child.”

Hannah Wilson (not her real name), from East Anglia, took her children, aged eight and 11, out of primary school because they were uneasy about the lack of Covid safety measures. Wilson and her husband had long Covid, including migraines, stomach cramps, tinnitus, leg pains and fatigue, for more than a year, and her son suffered for nine months. They don’t want the virus again.

“I think the head is very sympathetic and is clearly in a difficult position,” she says. “We don’t get supported with any work. There are no concerns about their education at home, but there is pressure on the head for us to return.”

She adds: “I have thought about exiting the system because of the pressure. If they were to fine me I would be very tempted to see them in court as I feel the way the government is behaving is unacceptable.”

A spokesperson for the DfE said: “As we learn to live with Covid, thanks to the success of the vaccination programme, there is no longer advice for vulnerable people to shield and it is right that children attend school full-time.

“The protective measures in place in schools follow scientific advice on how to strike the balance between protecting education and reducing transmission – including with enhanced ventilation and air cleaning units for classrooms that need them, and a vaccination offer for every child aged five and over with underlying health conditions.”