Over the course of the autumn term 2007 and spring term 2008 81,530 primary school pupils were absent for more than 48 half days, up from around 74,940 at the same time last year.
The number of persistent absentees in state-funded secondary school fell over the same period from 205,000 to 191,240.
Shadow schools minister Nick Gibb said: "It is the poorest pupils that are worst affected. Almost half of these children repeatedly skipping school are eligible for free school meals."
Manchester primary school children are the most likely to skip school, with 4.7 per cent of pupils classed as persistent absentees in the autumn term 2007 and spring term 2008.
The national average is 2.4 per cent. Rutland in the East Midlands has the lowest persistent absentee rate, at 1.1 per cent.
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