Children of key workers should only go to school on Monday as a "last resort", according to the Department of Education.
Education Minister Peter Weir said that only one parent needs to be a key worker for a pupil to attend school.
However he said children should only attend school if there was "no other viable option" for their care.
Most schools across Northern Ireland are expected to open on a limited basis from Monday.
Children of key workers as well as those with a statement of special educational needs (SEN), or other pupils who are vulnerable, can attend school.
At Enniskillen Royal Grammar School in County Fermanagh, principal Elizabeth Armstrong said a "small number of pupils" were in school on Monday morning.
Many schools spent Friday and the weekend contacting parents of pupils to find out who was likely to attend.
There is no set limit to the number of pupils a school can admit, as long as it is safe and they can observe Public Health Authority (PHA) guidelines on social distancing.
Some principals, though, have said they will not be able to open their schools on Monday due to concerns about the health and safety of staff and pupils.
Mr Weir acknowledged not all schools will be ready to open.
On Sunday, the Department of Education (DE) wrote to principals asking them whether they were going to open on Monday and in the days and weeks ahead.
The department also asked headteachers "whether you are willing to accept children and staff from other schools if needed."
The letter from the permanent secretary, Derek Baker, also said the DE would collect daily pupil and staff attendance figures.
Mr Baker thanked principals for their support in "trying to combat this unprecedented and serious threat we are all facing."
However, the Education Authority (EA) told parents school transport would not run as normal.
Parents have also been asked to send packed lunches for children as the usual school meals service will not operate either.
At the weekend the EA posted on social media that it had been "able to source a limited number of 50ml bottles of hand sanitisers."
It asked principals to contact them if they required them but also told heads they would be reimbursed if they bought urgently needed items themselves up to a value of £100.
One principal told BBC News NI they still did not know if hand sanitizer or other personal protective equipment (PPE) would be available in their school on Monday.
"We want to work together to support our communities but we equally want to keep everyone safe," they said.