Social distancing on buses may mean children entitled to free transport lose out when they return to schools.
Education Minister Peter Weir yesterday raised the issue yesterday in the assembly.
Mr Weir gave an update to the ad-hoc committee on the Covid-19 response on several announcements made over recent weeks.
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These include plans for the return to classroom learning, pay for sub teachers, summer schemes, support for childcare and free meals.
The committee was told that the provision of home to school transport in September would be an extremely complex and challenging area of work.
"Any form of social distancing will have a significant impact on the ability of the Education Authority to transport all children to school by bus or taxi," Mr Weir said.
"The Education Authority is making every effort to maximise the number of children that can be safely transported. However, if any restrictions remain in place in social distancing there is likely to be a substantial shortfall between the number of pupils who are eligible for home to school transport and the number of places available on vehicles.
"This impact will unfortunately be likely to be felt across all school sectors."
Mr Weir also told members that while there had been a lot of good work done on online learning, there would be a level of loss felt most in deprived areas.
He said he was to bring forward a project called Engage to provide literacy and numeracy support; mental health interventions; and the widening of nurture support for the 2020/21 academic year in socially deprived areas.
