Department for Education data shows up to 23.2 percent of children were absent from school for reasons linked to Covid-19 on July 15 – the day the Government body carried out its last snapshot survey.
Around 20.7 percent of children were self-isolating due to possible contact with a Covid-19 case, while the rest had a confirmed or suspected case of coronavirus, or were off as a result of Covid-related school closures.
The Government has been criticised for its rules around "bubbles" in schools, with teachers, parents and unions complaining the system caused widespread disruption to children's education, after pupils already missed out on so much in-person teaching due to the lockdowns.
Current rules say children have to self-isolate for 10 days if another pupil in their bubble – which can be an entire year group at secondary school – tests positive for Covid.
The latest snapshot shows up to 22 percent of secondary school pupils in North East Lincolnshire were not in class for reasons related to Covid, while up to 23.6 percent of primary pupils were missing school.
The figures have been adjusted to exclude students in Years 11-13, who were not expected to attend.
Teachers and school leaders were also impacted by Covid-related absences, with 10.2% missing work across school stages.
Education Secretary Gavin Williamson announced that the use of “bubbles” in schools in England will come to an end as the country eases lockdown restrictions.
Mr Williamson said it was up to individual schools and colleges whether they scrapped the bubble system ahead of the summer holidays, following the move to step four of the road map.
A record 1.13 million children in England were out of school for Covid-related reasons on July 15 – 14.3 percent of pupils from schools involved in the survey.
Geoff Barton, general secretary of the Association of School and College Leaders, said the data showed it had been an "extremely challenging end" to an already challenging school year.
He said: "The Government must put a much greater focus on putting an end to educational disruption in the autumn term and provide more support to schools and colleges."
Paul Whiteman, general secretary of school leaders’ union NAHT, said while absence levels were mainly due to pupils isolating, there had also been a "sharp" rise in pupils testing positive for Covid-19.
He added: "Removing the requirement for close contacts to automatically self-isolate will no doubt reduce absence figures, but it is important the Government does more to actively reduce case numbers amongst children and transmission in schools."
A DfE spokesman said: “Where children needed to isolate last term, schools were required to offer immediate access to high-quality remote education.
“As of step 4, schools no longer need to operate a bubble system, and from August 16 pupils will not need to self-isolate should they come into contact with a positive case, in line with the position for wider society.”