The leader of Greenwich Council has said he has “no choice” but to ask schools to remain open following threats of legal action from the Government.

The local authority has agreed to withdraw its advice to schools in the south-east London borough to move to online learning for the last few days of term amid rising Covid-19 rates in the capital.

The decision comes after Education Secretary Gavin Williamson told the Labour-run council on Monday evening to keep schools open to all pupils until the end of term or it will face legal action.

In a statement, Greenwich Council leader Danny Thorpe said: “With Covid-19 cases rising rapidly in the borough, I cannot agree that this is the correct choice for our schools.

“However, I also cannot justify the use of public funds to fight the decision in the courts.

“Consequently, I have no choice but to ask our schools to keep their doors open to all students rather than just continuing with online learning.”

Mr Williamson welcomed the decision as he said children’s education was a “national priority”.

Schools in Greenwich had been told to switch to remote learning for most pupils from Monday evening in a letter sent out by Mr Thorpe on Sunday.

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

Schools Standards minister Nick Gibb has written to both councils in London to remind them of the importance of keeping schools open, but no legal direction has been taken against the local authorities at this stage.

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

Consequently, I have no choice but to ask our schools to keep their doors open to all students rather than just continuing with online learning

On Monday evening, Mr Williamson issued a temporary continuity direction to the London Borough of Greenwich demanding it withdraws letters to heads and parents which advised schools to close.

The direction said it was enforceable by Mr Williamson making an application to the High Court or the county court for an injunction if the council did not comply by 10am on Tuesday.

In a statement on Tuesday morning, Mr Thorpe said: “The council has issued the following response to the Government, which outlines our serious concerns about forcing our students to attend school in person and our intention to reluctantly comply with the Secretary of State’s directive.”

Kate Green, shadow secretary of state for education, said it was “pretty unhelpful” for the row to have resulted in the Secretary of State issuing a legal instruction to Greenwich council ahead of Christmas.

Speaking during a webinar held by the Child Poverty Action Group, she said: “I don’t see why they can’t just get round the table and negotiate a sensible way through the last couple of days of term.”

Geoff Barton, general secretary of the Association of School and College Leaders (ASCL), said: “The Government may find it has won a hollow victory in its squabble with Greenwich council over end-of-term arrangements.

“It has compelled direct classroom teaching for the last few days of term but we would not be surprised if many parents simply keep their children at home given the evident concern over Covid-19 infection rates.”

Jenny Whitmore, who has a 14-year-old son at a school in Greenwich, told PA news agency that she was happy to keep her son at home this week as the cases of Covid-19 in the area were “very high”.

She said: “So for the sake of a few days it works better for us as a family. Our school is still open for those children that want to go in and keep their routine.

“It’s down to personal choice, and we agree with the decision that Greenwich council made and believe they were putting children’s, parents’ and staff’s health first.”

Children’s education is a national priority and this Government has acted in the interest of children since the start of the pandemic

In Basildon in Essex, eight out of nine secondary schools have already moved to full remote education.

A number of independent schools – including the Prime Minister’s former school Eton College – have switched to online lessons and ended in-person teaching early amid a number of Covid-19 cases.

Downing Street has defended the Government’s determination to keep state schools open ahead of the end of term despite rising coronavirus cases.

The Prime Minister’s official spokesman said: “We have been clear throughout on the importance of schools, both in terms of the learning that children require but also the development and mental health gains it brings by being able to attend school.

“We have been clear that it’s in the best interest for all children to attend.”

Asked whether that message applied to private schools, the spokesman said: “The Government thinks that all schools should remain open for children and that’s the best place for them to be.”

Education Secretary Gavin Williamson said: “Children’s education is a national priority and this Government has acted in the interest of children since the start of the pandemic.’

“I welcome Greenwich Council’s decision today, and the Regional Schools Commissioner and her team will continue to work with schools in the borough, as we are with schools across the country, to make sure they have the support they need to continue face to face education right up to the last day of term.”