A further 84,000 did not go in on Thursday as they had a suspected case, the statistics from the Department for Education (DfE) show.
An estimated 5,000 could not go due to restrictions on attendance to limit a Covid-19 outbreak, while thousands more were isolating.
The Association for School and College Leaders called the latest statistics “grim”.
Geoff Barton, the union’s leader, said the data showed “a big increase” in the number of pupils off school due to “the continuing havoc caused by coronavirus”.
“We are hearing from schools where there are 10 per cent or more of pupils absent and where staff are also off work because of the virus,” he said.
“Teaching and learning is very difficult in these circumstances and it is clear that the educational disruption of the past 18 months is far from being over.”
In total, the government estimates 204,000 pupils in England – 2.5 per cent of the country’s school population – were absent due to a Covid-related reason on 30 September.
This was a 67 per cent jump in the number of absences linked to coronavirus compared with two weeks before.
On 16 September, 122,000 pupils were out of school due to a Covid-related reason. As with the latest figures, the majority of these absences were because of a suspected or confirmed case of coronavirus.
Children no longer have to isolate after coming into contact with someone with Covid.
Following the release of the attendance figures, Kate Green, the shadow education secretary, said: “The government must not allow another year of children’s learning to descend into chaos with pupils constantly in and out of school.
“Ministers should have acted months ago to put ventilation systems in place in our schools and should be doing everything possible to vaccinate teenagers. Yet once again the government has been too slow to act and children are left feeling the consequences.”
A DfE spokesperson said: “We are committed to protecting education, which is why the safety measures in place strike a balance between managing transmission risk with regular testing and enhanced ventilation and hygiene, and reducing disruption to face-to-face education.
“We are working with parents and school and college staff to maximise students’ time in the classroom – encouraging uptake of testing and the vaccine for 12-15-year-olds and contracting specialist attendance advisers to work on strategies to improve attendance where problems are identified.”