Children identified as vulnerable and therefore entitled to a place in emergency school provision during the coronavirus outbreak failed to turn up on Monday, raising concerns among headteachers about their safety.

On Friday, schools closed their gates indefinitely to all students, apart from the children of key workers vital in the fight against Covid-19 and those identified as vulnerable, either because they have significant special educational needs or have a social worker.

School leaders worked frantically over the weekend, contacting parents to find out which pupils were in need of a place and to encourage families where possible to keep their children safe at home, amid complaints of a lack of clarity and leadership from central government.

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Those encouragements appeared to have been heeded on Monday morning, with some headteachers reporting that staff vastly outnumbered pupils. In one secondary school there were five teachers for every student, so staff were sent home. But there were concerns that vulnerable children were among those who stayed away.

There had been fears that schools providing a skeleton childcare service would be inundated with students, but in the event some multi-academy trusts reported absence rates of up to 97%.

“We are very grateful to parents,” said one school leader. “But we are really worried, particularly for our most vulnerable children. We are very concerned we are not seeing those children.” One trust said around four out of five children identified as vulnerable failed to attend.

Vic Goddard, the co-principal of Passmores Academy, in Harlow, Essex, spoke for many heads when he said he felt both scared and angry about the challenges facing headteachers, and complained about lack of leadership from the government.

In a tweet on Sunday, he said: “Been asking for help from govt all day. I am angry, frustrated and scared. I’m being asked to make life and death decisions for my own and others’ families.”

Teaching unions called for testing of school workers and greater clarity on how to keep staff and students who continue to attend school safe. Paul Whiteman, general secretary of the National Association of Head Teachers (NAHT), said: “From masks or other PPE (personal protective equipment), to distancing children from each other, to sufficient supplies of soap and hand sanitiser, schools urgently need answers to their questions about effective safety measures.”

According to an NAHT survey of more than 3,000 members, 94% of schools opened to provide emergency cover, 94% of those had less than 20% of their usual children attending and almost six out of 10 (58%) had less than a quarter of their usual teaching staff.

Geoff Barton, the general secretary of the Association of School and College Leaders, said: “Schools are reporting that the number of pupils arriving is manageable. We are grateful to parents for their understanding.” In Devon, schools were providing their safety goggles and glasses from science departments to local hospitals for nurses on the frontline.

Richard Sheriff, executive headteacher and chief executive of the Red Kite Alliance, which runs nine primary schools and four secondary schools across Leeds and north Yorkshire said demand for secondary schools was low, but children were turning up at primaries in greater numbers.

At Temple Moor high school in Leeds, just eight students out of 1,200 turned up first thing on Monday morning, where they were dramatically outnumbered by around 40 staff, while at Western primary school in Harrogate, 44 children walked through the school gates.

Sheriff said he was concerned about vulnerable children who did not turn up for school on Monday. “Headteachers and members of staff are on the phones trying to make contact with those children and their families,” he said.

“It’s a weird day,” said Sheriff. “It’s really strange. The streets around schools are normally busy, you can’t get parking. There’s always a cluster of mums and dads outside chatting, with their buggies. Today there’s none of that … Those [children] that are turning up, they look awkward and afraid.”

Elsewhere there were concerns that some parents were sending in children who should not be there.

Goddard said he had turned four or five families away where just one parent was a key worker and the other parent was at home. The government has said that families with at least one parent who is a key worker are entitled to a school place, but Goddard said it was “unsustainable” over a long period.

Just 14 children out of 420 turned up at Hartford Manor primary school in Cheshire, after initial fears that as many as 130 might claim a place. “We’ve very much been on the front foot on this one,” said headteacher Simon Kidwell, who said all parents had been asked to consider: “Is your job corona critical?”

Kidwell described his new-look school, with no uniforms, no lessons and very few students. “It just feels very calm and lovely – a bit of an oasis. Children have never had this experience before, where they get to just play in their primary school. It’s going to be strange. I’m no longer a headteacher, I’m a leader of a play scheme.”

But he warned about the urgent need of keeping in close contact with all pupils at home including those with special needs. “If we don’t get this right it’s going to rip through families and it’s going to rip through communities.”