More than 122,000 children in England were out of school for Covid-19 related reasons last week, Government figures show.

About nine in 10 pupils were in class on September 16, according to the first analysis of attendance figures since schools fully reopened this month.

The Department for Education (DfE) estimates 1.5% of all pupils – around 122,300 children – were not in school for Covid-19 related reasons on Thursday last week.

The figures include 59,300 pupils with a confirmed case of Covid-19, 44,600 with a suspected case and 15,900 absent due to isolation for other reasons.

A further 2,000 pupils were off due to attendance restrictions being in place to manage an outbreak and 500 did not attend as a result of school closures due to Covid-related reasons.

It comes as schools in England no longer have to keep pupils in year group “bubbles” to reduce mixing and children do not have to isolate if they come into contact with a positive case of Covid-19.

Instead, they need to get a PCR test and isolate only if positive.

Headteachers’ unions have warned that educational disruption remains “significant” and some schools are already struggling to keep classes open.

Some 91.9% of students were in class on Thursday last week (September 16), according to the DfE analysis. In comparison, approximately 87% of students were in class on September 17 last year.

All secondary school and college pupils have been invited to take two lateral flow tests at school, three to five days apart, in England on their return.

Schools and colleges are being encouraged to maintain increased hygiene and ventilation and secondary school and college pupils have been asked to continue to test twice weekly at home.

Geoff Barton, general secretary of the Association of School and College Leaders (ASCL), said: “It is clear from the fact that over 100,000 pupils were absent from school last week with a confirmed or suspected case of coronavirus that educational disruption remains significant.

“We are hearing of schools where significant numbers of pupils are absent.

“We are hopeful that the vaccination programme for 12 to 15-year-olds will help to reduce this level of disruption. However, the Government must also take more action to support schools and colleges.”

The Government should launch a public information campaign to encourage twice-weekly home-testing among pupils and provide funding for high-quality ventilation systems in schools and colleges, the union has said.

In July, figures showed that a record 1.13 million children in England were out of school for Covid-19 related reasons towards the end of term.

Rules at the time said children had to self-isolate for 10 days if another pupil in their bubble – which can be an entire year group – tested positive for Covid-19.

Paul Whiteman, general secretary of school leaders’ union NAHT, said the latest numbers reflect changes to government policy which requires fewer pupils to self-isolate when there is a positive case in school.

But he added: “It’s important to note that these national figures mask some significant issues arising at a local level, and we already know of schools that are struggling to keep classes open due to outbreaks occurring.

“It is crucial that both central and local government are now on high alert and are ready to react quickly if and when cases rise rapidly or outbreaks occur. The next few weeks will be crucial.”

Kate Green, Labour’s shadow education secretary, said: “The Conservatives’ chaotic failure to plan ahead or to listen to Labour, parents and teachers and get ventilation and mitigations in place saw over 122,000 children out of school again last week. This is not good enough.

“The Conservatives have left schools in a mess, the new Education Secretary urgently needs to set this right.”

Education Secretary Nadhim Zahawi said: “My priority is to make sure children are in school and back to face-to-face learning. That’s the best place for them to be, so it’s fantastic to see more than 91% of them back in the classroom with their teachers and friends, compared to 87% this time last year.

“That’s down to the hard work of teachers, support staff as well as families whose efforts have been heroic in making sure children can get back to school safely.

“The rollout of the vaccine to those aged 12-15, which started this week, is another significant step in building the walls of protection from the virus across society.”