The proportion of children off sick rose to 7.5% in the week commencing 5 December - up from 6.1% the previous week and 2.6% at the start of the term.
Overall absence rates up to that week surpassed the whole of the 2021 autumn term, when Omicron was taking hold.
A head teachers' union said it was "concerning" for health and education.
The increase in absence has been driven by illness, the Department for Education said, and is "in line with recent increases in rates of seasonal flu and other seasonal respiratory illnesses".
The illness absence rate for the whole autumn term up to the week commencing 5 December was 4.3%.
This is slightly lower than the 4.4% recorded across the 2021 autumn term - although it is expected to rise in the data for the final week of term, to be released in the New Year.
However, the overall absence rate recorded for the 2022 autumn term up to the week commencing 5 December was 7.3% - higher than the 6.9% recorded across the whole of the autumn term in 2021.
That is partly due to all types of unauthorised absence having increased this term, compared with both pandemic and pre-pandemic levels.
Cases of flu have been on the rise in recent weeks, according to the UK Health Security Agency (UKHSA), while the increase in cases of Covid has been "modest".
Flu was most prevalent among those aged between five and 14 in the week commencing 5 December, the UKHSA said in its most recent report.
Geoff Barton, general secretary of the Association of School and College Leaders, said staff had worked hard in the run-up to Christmas to keep attendance levels high.
"This has been especially challenging in recent weeks, however, with illnesses including Strep A and Covid-19 affecting attendance alongside flu and winter colds," he said.
"While schools have managed this situation as best they can, the rise in absence rates is concerning from both a health and education point of view."
Absence due to illness remained relatively stable - between 2.5% and 2.9% - from 2016 to 2019. But schools faced massive disruption due to Covid in the autumn term of 2020.
In Wales, attendance statistics released on Wednesday showed a higher rate of overall absence than in England, with 10.3% of school sessions missed so far this academic year.