Stringent social distancing in schools will be difficult to achieve when they reopen, according to the education minister.
Peter Weir said it would result in a "significant" impact on the school day.
The minister made the comments in a letter to the teaching unions in Northern Ireland setting out what he called an "education restart programme."
Schools in England began admitting more pupils on 1 June.
But Mr Weir has previously said schools in Northern Ireland should begin a phased re-opening in the second half of August.
The minister said that measures such as pupils attending school part time and some year groups being a priority would remain in place "for as long as is necessary."
Mr Weir was writing in response to a document from the Northern Ireland Teachers' Council (NITC) setting out its contingency planning for re-opening schools after the summer break.
The NITC represents the five teaching unions and highlighted a wide range of measures.
The unions said comprehensive testing and contact tracing needed to be in place before schools could reopen.
"As teachers will be at greater risk of infection on return to school, we seek priority and regular access to testing for all school employees as part of a community testing programme," they said.
They called for comprehensive risk assessments to be carried out in every school and for them not to re-open if measures to control risk were not in place.
"It may be necessary to have a reduced pupil intake on school reopening unless social distancing is viable," the NITC said.
"In post-primary schools priority should be given to those year groups who are studying for external qualifications."
The NITC said that parents should be able to enter schools "by appointment only".
"Schools will have to put in place procedures for the arrival and dismissal of pupils to take place outside the school building in a safe space.
"Extension of lunch breaks, staggered breaks, distribution of lunches to rooms rather than gathering of pupils in the normal way should be considered."
The unions said the Department of Education (DE) should pay for appropriate protective equipment like masks for staff and pupils, if it was needed.
They also said that due to likely staff absences, the DE should fund the employment of substitute teachers and support staff rather than the costs being met by schools.
In his letter, Mr Weir said: "It is important that we begin to see recovery and a process of phased reopening of our schools."
But he said that would be guided by medical and scientific advice, and the timing of schools re-opening would be determined by circumstances, not dates.
As social distancing will be difficult to achieve, Mr Weir said, measures put in place would include "phased returns, prioritisation of learners and ongoing blended learning".
"We will consider and implement 'new school day' arrangements for as long as is necessary, considering practical arrangements in schools relating to transport, school meals, class sizes, daily routines, curriculum delivery and extracurricular activities," he said.
The minister said he had established a new board chaired by the DE permanent secretary to manage the restart programme.
"I recognise that schools will want to make preparations for restart in August, particularly during the month of June, and I would aim that the work to deliver the priorities outlined above will be progressed during the remainder of this term," he concluded.
The principal of one of Northern Ireland's biggest schools, Methodist College in Belfast, previously said that it could only reopen "in a meaningful way" if social distancing guidelines changed.