Secondary school attendance overall dropped to 83 per cent last week, down from 87 per cent the previous week.
A spokesperson for the DfE said: “The drop in attendance is mainly due to the increased number of pupils self-isolating due to potential contact with a case of coronavirus.”
School attendance varies widely across the country, with some areas hit worse than others.
Hull’s director of public health Julia Weldon warned on Tuesday more than half of schools in the city have seen closures in some year groups due to coronavirus.
Headteachers in Hull have asked the Health Secretary Matt Hancock to allow them to close for all but vulnerable children and the children of key workers as they struggle to cope with staff absences.
They said they want to keep schools open but that “as a matter of some urgency” some need to be able to restrict attendance “in order to maintain high-quality provision and the morale of all those in education”.
The city’s Labour MPs warned Mr Hancock coronavirus rates are at “alarming” levels in the community adding: “There is a concern that if children of key workers cannot be prioritised for attendance there will be a major threat to the infrastructure in the city.”
A legal duty on schools to provide good quality remote education for self-isolating pupils came into force last month.
The Government used emergency powers to issue a directive to schools to ensure children at home have immediate access to remote education that it “aligns as closely as possible” with what their peers learn in the classroom.
However, the Scientific Advisory Group for Emergencies (Sage) has said that prolonged periods of remote learning are “likely to result in poorer educational outcomes” for pupils, according to international studies.
A DfE spokesman said: “Over 99 per cent of schools have been open every week since term began and millions of pupils are continuing to benefit from being in school.
“The Chief Medical Officer remains of the view that schools should remain open, and has highlighted the damage caused by not being in education to children’s learning, development and mental health.”