There are now concerns that thousands of youngsters in more deprived neighbourhoods are being placed at a disadvantage for "now and in the future”.
Schools returned in August after having been closed since March as a result of there pandemic, but attendance levels have fluctuated. There was a surge in absenteeism in late August as parents took a cautious approach to any sign of symptoms.
The average attendance in the past month in schools in more deprived areas was 88.1 per cent, official statistics have revealed. This compares with attendance levels at schools in more affluent areas of 95.3 per cent - a gap of more than 7 per cent, accounting for more than 40,000 pupils.
On certain days, the gap in attendance rate between the two quintiles was 11 per cent.
The research was conducted by parents group UsForThem Scotland, which said it provided more evidence that children in areas of poverty have been worst-hit by pandemic and subsequent lockdowns.
Jo Bisset, organiser for UsForThem Scotland, said: “It’s been long suspected that children in the poorest areas have been worst-hit by coronavirus – now these statistics prove it.
“Schools should be more-or-less running as normal, yet in the last month more one in ten vulnerable youngsters have missed out on vital education.
“This obviously places them at even more of a disadvantage for now and the future.
The Scottish Government figures – which were analysed from September 14 to October 13 – show the gap between rich and poor has extended as a result of Covid-19.
Last year, the overall attendance rate for the poorest 20 per cent was 90.4 per cent, compared to 95.3 per cent for the wealthiest – a gap of 4.9 per cent.
Ms Bissett said: “The Scottish Government makes the right noises about keeping schools open even when other parts of society are closed down.
“But that’s not translating into action for children from the least privileged backgrounds, and that will have hugely negative consequences.”
It emerged last month that more than 100,000 pupils in Scotland are absent from school with attendance down to 84.5 per cent, according to Scottish government figures.
Data collected from local authorities shows that more than 15.5 per cent pupils were off school on August 28, as absenteeism soared in the weeks after schools returned.
Only 22,821 of the absences are recorded as "Covid-19 related".
Ministers said at the time it was common for other viral infections to circulate after a "prolonged break" away from school, but teaching union the EIS said many parents were "erring on the side of caution" and keeping children who had cold symptoms off school.
A controversial system for awarding national five and Higher grades had been axed after it emerged the "moderation" approach disproportionately penalised youngsters from more disadvantaged backgrounds.
A Scottish Government spokesperson said: “We appreciate that this has been a difficult time for families and pupils.
"After an initial dip when schools reopened, overall attendance rates are now similar to average levels in previous years.
"We are grateful to all the teachers, school staff and many others who have worked hard to return some normality.”