More than one in 10 pupils in Northern Ireland were not in school during the second week of the new term, Department of Education figures show.
The department says 88.9% of pupils were in school during the week from 6 September to 10 September.
The attendance figures include primary, post-primary and special schools, but not pre-schools.
They suggest 3.1% of pupils - about 10,000 - were learning from home due to self-isolation or social distancing.
That is the highest proportion of pupils recorded as self-isolating by schools since all pupils returned to face-to-face teaching at Easter.
However, 8% of pupils were marked absent by schools for reasons not due to self-isolation or social distancing in the week commencing 6 September.
While the percentage of pupils in school was at 94% during the first week of the new 2021/22 school year that fell to 88.9% in the second week.
Highest rate of absence in special schools
In some schools hundreds of pupils were out of class in self-isolation after coming into close contact with positive Covid cases.
On Friday, the Public Health Agency (PHA) took over primary responsibility for contact tracing in schools.
Health Minister Robin Swann and Education Minister Michelle McIlveen said the Public Health Agency (PHA) would take a "more targeted approach" to contract tracing.
The Department of Education attendance statistics suggest that 4% of pupils in grammars were not in school for Covid-related self-isolation or social distancing in the week beginning 6 September.
But the highest rate of overall absence was in special schools with over 11% of pupils marked absent.
In primary schools 7% of pupils were absent while in non-grammars just over 10% of pupils were absent.
However, the majority of pupils were recorded by schools as being absent for reasons other than Covid-related ones.