She also told parents that opening windows was the most effective way of helping ventilation in classrooms and added that she had encouraged schools to be flexible with their uniform policies.
She also said that contingency arrangements are in place for qualifications to be awarded on teacher assessments if exams have to be cancelled this summer.
Ms McIlveen’s letter said: “We are now in the midst of another phase of the pandemic, with the new Omicron variant leading to significant case numbers across our communities.
“Case numbers in children and staff are likely to continue to reflect those in the community and we can expect some disruption in the coming weeks.
“My focus has been, and remains, on the continuing provision of education within our schools for all our children.
“I want to reassure you that the NI Executive continues to have a shared objective to keep schools safe and open, because the best place for children and young people is in school.”
Ms Ilveen said there had been much discussion on the importance of ventilation in reducing Covid risks.
She added: “I have been advised by health colleagues that natural ventilation, by opening windows, is the single most effective measure.
“The installation of air filtration units would not, for example, allow schools to close the windows as natural ventilation remains paramount.
“Opening windows periodically can, at this time of year, result in cooler classrooms.
“Schools will do their best to keep classrooms at an appropriate temperature and I have encouraged them to be flexible in their uniform policy to ensure pupils are able to be comfortable.”
Her letter went on to say that over the next few weeks schools may not be able to continue to operate as normal.
She said: “There may be staff shortages due to illness or self-isolation and there could be significant numbers of pupils absent as well.
“Schools have plans in place to deal with these issues and this means your child may experience some changes to their normal school day.
“This could include the need to use more substitute teachers, to prioritise teaching for those pupils sitting key exams, or in some cases to move pupils to remote learning for short periods until pressures have eased.
“I have also asked student teachers to provide additional help in the coming weeks.”
The minister said the intention is for GCSEs and A-levels to go ahead this summer, but that students would have to take “fewer examinations”.
She continued: “Should the public health situation change and public examinations have to be cancelled, I have agreed contingency arrangements for qualifications to be awarded on the basis of teacher judgment, as in 2021.
“All of our young people will be enabled to complete their qualifications and progress to the next phase of education, employment or training.”
Meanwhile, a further four people who previously tested positive for Covid-19 in Northern Ireland have died, the Department of Health has said.
Another 2,954 confirmed cases of the virus were also recorded in the latest 24-hour reporting period.
On Friday there were 402 Covid-positive patients in hospital, with 30 in intensive care.
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