About a million children - one out of every eight pupils - were absent from schools in England last Thursday, as Covid cases rose.
The official figures also show staffing problems worsening, with a quarter of schools seeing teachers and leaders' absence rates above 15%.
Across England as a whole, about 9% of teachers were absent.
The government has recently removed the requirement for pupils to wear masks, after loosening Covid restrictions.
Of the one million pupils (12.6%) absent, 415,000 were out of school for Covid-related reasons.
Also on 20 January, 47,000 teachers and school leaders were absent - 3,000 more than two weeks previously - half for Covid-related reasons.
National Association of Head Teachers general secretary Paul Whiteman said: "Covid absence figures for pupils are the worst they have been this academic year.
"Schools are struggling to keep things running, with nearly 10% of their staff off, on average - but for some, this is much higher.
"Our members are repeatedly telling us that they are having to drop everything to find cover and that just keeping things going is a challenge."
And this was putting huge pressure on pupils in exam years.