Closing schools could see children “pay the long-term price”, the Ofsted chief inspector has warned as the Government faces a battle with councils.

Amanda Spielman has supported ministers’ decision to keep schools in England open until the end of term as she warned that “last-minute decisions” to close schools could affect children and working parents.

Education Secretary Gavin Williamson has told the Labour-run Greenwich council to keep schools open to all pupils this week or it will face legal action.

Schools in the south-east London borough were told to switch to remote learning for most pupils from Monday evening in a letter from council leader Danny Thorpe.

Leaders at two other Labour-run local authorities – Waltham Forest and Islington – have also advised schools to move to online learning for the last few days of term amid rising Covid-19 rates in the capital.

London mayor Sadiq Khan has also called on the Government to consider closing all secondary schools and colleges in the capital early and reopen later in January due to coronavirus.

But on Monday night, Mr Williamson issued a temporary continuity direction to the London Borough of Greenwich demanding it withdraws letters to headteachers and parents which advised schools to close.

Greenwich council has said it is seeking legal advice and will respond to Mr Williamson on Tuesday.

Asked if schools should be kept open in England, Ms Spielman told BBC Radio 4’s today programme: “I do believe it’s the right thing to do, rather than taking very short-term decisions to close…

“Arranging child care at short notice – we could be taking doctors, nurses off shift, out of vaccination clinics. Inadvertently shooting ourselves in the foot.”

She added: “We are in a really difficult situation where people are having to weigh up short-term concerns about health risks and long-term concerns about children’s education. It’s very difficult to do that.

“It is so easy to call for closures, and forget the long-term price that children pay. We need clarity, consistency, not last-minute decisions.”

Her comments came as a report from the watchdog concluded that repeated periods of isolation have “chipped away” at the progress that pupils have been able to make since returning to school.

Geoff Barton, general secretary of the Association of School and College Leaders (ASCL), has described the fight between national and local government as “pretty squalid” as he expressed outrage that some headteachers had been threatened with legal action over refusing to keep their schools open.

He told BBC Breakfast: “How dare we treat our public servants who are trying to do their best in difficult circumstances to keep education going – how dare we have them treated like that?”

Mr Barton added: “It’s pretty squalid, don’t you think, that here we seem to have turf wars between the national and local government, and in the middle of it the people I represent – headteachers.

“I think we want to look back and think we did the right thing for our schools and college communities. Who is placed to decide what kind of online learning we can provide?”

Dr Mary Bousted, joint general secretary of the National Education Union (NEU), said: “We condemn the decision of the Secretary of State to pursue legal routes. This is a desperate move from government ministers who have lost the plot. Rather than resorting to legal action, ministers should be supporting heads to make professional judgments on the safety, or otherwise, of their school remaining open.

“I am hearing from heads who have high numbers of staff isolating, combined with Covid clusters in their school which mean that whole year groups have to stay at home. The situation is chaotic and unsustainable.”

But Calum Semple, professor of outbreak medicine at the University of Liverpool and a member of the Scientific Advisory Group for Emergencies (Sage), said experts are “not seeing an increase in disease severity or numbers amongst school teachers, that has to be borne in mind”.

He told BBC Breakfast: “We do appreciate that teenagers are capable of catching the virus, and transmitting it amongst themselves and taking it home, but we’ve made a very important political decision that schools need to be kept open because we cannot throw away a generation of broadcasters, lawyers, even politicians who are in the making, and they need to be educated and be ready to take up the mantle in years to come.

“So, schools have been considered to be essential. It shouldn’t be perceived that schools are the only place where amplification is happening.”