Schools that have battled to stay open during swine flu outbreaks have warned that they are being unfairly penalised by the Government for high absence rates.
Official statistics up to spring show a rise in the number of pupils missing school, and local authorities fear thousands more did not attend lessons in the early summer and autumn.
Schools that remained open say it is unfair that their depleted numbers during these periods will count against them - unlike schools which closed, where the absences are not recorded in the official statistics.
The Department for Children, Schools and Families only asks for the number of authorised and unauthorised absences and not the reasons behind them. Ofsted use absence rates to make judgments about schools.
The same applies to schools that managed to remain open during the snow storms of February this year.
Sandwell and Nottingham have the highest numbers of children in the country missing school.
Unauthorised and persistent absence rates in Nottingham were around twice the national average.
In Sandwell, unauthorised absences are double those of most other local authorities, and authorised absences are 1 per cent higher.
Sandwell Metropolitan Borough Council cabinet member for schools Ian Jones said he thought this was due to the council's policy of keeping classrooms open during the snow and frost in February - which hit the area particularly badly.
Pupils also suffered heavily from norovirus. In addition, Sandwell is at the epicentre of a swine flu outbreak, so absence figures are likely to be even higher for the summer and autumn terms this year.
"We don't have a blanket policy of closing schools in certain situations, as some local authorities do, so this must account for their absence rates being lower," Mr Jones said.
"All we want is for the Government to treat like with like. Statistics don't show everything and it's almost like schools that close are rewarded."
Wolverhampton was also hit by snow and swine flu. The city council cabinet's member for education, Gillian Fellows, said teachers would soldier on if events this winter affected attendance.
"Schools have got to remain open if possible, but we need to leave this up to the teachers," she said.
Some religious festivals, such as Eid, celebrated by Muslims at the end of Ramadan, fell mid-week this year, and the Association of School and College Leaders thinks this will also add to poor attendance figures when new statistics are released.
"Our members in areas with high numbers of ethnic minority pupils have been quite considerably affected," said deputy general secretary Martin Ward.
"Official figures never reflect the actual circumstances. But there is a perverse incentive to close outright rather than keep open.
"It makes it look like shutting is the right thing - something most schools try hard not to do."
Councils are now providing a weekly update to Government about swine flu rates. In the summer term, 136 schools closed, on average for a week, after an outbreak - mainly as a result of advice from the Health Protection Agency.
The situation changed when it became clear that keeping children away from school would not contain the spread of the virus, but there were some school closures because of staff shortages.
This term, up to October 21, four schools have closed because of swine flu - all as a result of staff shortages.
Two have reopened after being closed for a week, the other two have closed within the last week.
A DCSF spokesman said its focus was on persistent absence, and teachers would be able to explain the reasons for high absence to Ofsted and the National Strategies.
"It is up to headteachers to make professional and common-sense judgments about marking absences as authorised or unauthorised during very severe weather," he said.
"If a school which remains open is satisfied that the reason a child could not get to school was the adverse weather, then that absence should be authorised.
"If a school judges the child could have got to school, then that absence should be unauthorised."
Gone missing: Regional variations take their toll
In England, a total of 72, 600, an average of 2.2 per cent of all pupils, are classed as persistent absentees.
But this masks big regional differences - for example, in Nottingham almost 5 per cent and in Sandwell 4 per cent of children miss lessons regularly compared to 1 per cent in Rutland and Bracknell Forest.
Around 5.4 per cent of half-days were missed in autumn 2008 and spring 2009; 4.8 per cent of the absences were authorised and 0.65 per cent were unauthorised.
Warrington has the lowest level of absences in the country - 4.61 - after a "big effort" to change the culture of education in the town.
Families of pupils who refused to come to school have been given extra help and teachers have made additional efforts to praise children with good attendance records.
"It's been about changing the ethos and making school good, as well as giving a strong message about how important it is for children's futures," said Councillor Sheila Woodyatt.
"Teachers also know they have our backing and enthusiasm."