More special schools have said their pupils can only attend part time for two days a week on a temporary basis.
Oakwood and Glenveagh Special Schools in Belfast have told parents they are moving to "blended learning" for a period.
That follows Fleming Fulton's decision to introduce a similar arrangement.
Sperrinview Special School in Dungannon had also moved to part-time attendance for pupils, which is being kept under weekly review.
The Education Minister, Peter Weir, decided on 5 January that special schools should remain open for all pupils.
Some parents of pupils with special educational needs had previously warned of the damaging impact of school closures on their children during the lockdown from March to June 2020.
Attendance data published by the Department of Education (DE) has shown that a significant number of pupils and staff have not been able to attend special schools since the start of the new term in January.
In a letter to parents of pupils, the principal of Oakwood School, Tish McCann, said that from Monday, 25 January pupils would attend on either Monday and Tuesday or Thursday and Friday.
She said the decision had been taken "following a rigorous review of our risk assessments".
"We have determined the risks can only be reduced further by decreasing the daily numbers mixing within classes and school transport," she wrote.
"We continue to do our utmost to keep our school open and our pupils and staff safe.
"While we understand that this may prove challenging for some children, we believe that it is a better approach than the situation we are currently in.
"We are introducing these measures in order to try to provide families and children with a measure of routine and certainty in these uncertain times."
In a similar letter, the principal of Glenveagh Special School, Anne Moore, told parents that the school had had to close classes to pupils at short notice in recent weeks.
"It is unlikely that this situation will improve over the coming weeks," she wrote.
"We appreciate that this has not been helpful for children or their families."
She said that pupils in Glenveagh would also attend on either Monday or Tuesday or Thursday and Friday on a temporary basis.
She said with lower numbers in school: "We can reduce the risks of transmission of Covid-19 in the light of the fact that most pupils are unable to socially distance or wear face coverings."
However, she told parents that the school would let pupils who find it "particularly challenging to remain at home" to attend four days a week, as well as the children of key workers who had no alternative.
Both Oakwood and Glenveagh said they would also provide online resources so that pupils could learn at home.
In the Republic of Ireland, schools for children with special educational needs have not reopened due to a dispute between the government and teaching unions.