The Department of Education has revealed that almost one in 10 pupils did not attend school during the first full week of term earlier this month.
The figures came to light after SDLP MLA Pat Catney and Sinn Fein MLA Karen Mullan asked Education Minister Peter Weir to detail attendance rates.
As of September 7, 91.3% of pupils were in attendance at primary schools, while 8% of students in a post-primary setting were absent.
The overall attendance rate was 91.6% across all schools.
That figure was down 0.7% compared to the 2019/20 academic year.
The Department of Education could not confirm if the attendance figures had dropped because of the coronavirus pandemic as it does not hold information about why pupils are absent from class.
Mr Weir said earlier this week his department would not take a punitive approach to parents who did not send children to school because of Covid-19 fears.
Attendance rates in Northern Ireland at the start of term were higher than in England.
The overall attendance rate on September 1 was 94.6%, but it fell by the three percentage points the following Monday.
The attendance rate during the week of September 7 was highest in grammar schools, with 94.2% of pupils attending. It was lowest in special schools, at 85.2%.
Separate figures released by the department on September 9 revealed that there had been 88 positive Covid-19 cases in 64 schools and that almost 95% of teachers were working in classrooms.
Commenting on the data, Lagan Valley MLA Mr Catney said he thought the figures would have been much worse but admitted they were still "not good".
"The virus could be part of the reason. I have been around a few schools this week just to see how they're doing," he added.
"They're staggering the pupils coming and going out and they're changing times for different classes and different year groups to go out of class.
"They're trying to keep them wrapped up in their bubbles.
"There's a lot of parents definitely holding children back, but we want to try and keep our schools going.
"We have the guidelines. Yes, they may well have been slow, but teachers are doing their best and doing a mighty job.
"The onus is on all of us to protect our children, to protect our teachers and to protect the whole society. There is a wee bit of faith that has to be built into the system here to try and get back to normal as soon as possible."
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