Secondary school buses are to run at only half capacity.
The government had previously said that all school buses would be able to run as normal and at full capacity.
The u-turn comes the week before many schools are due to welcome students back.
In a statement, the Department of Education says the decision has been made in light of the latest advice from the National Public Health Emergency Team.
The Department says "Discussions are already underway with Bus Éireann in respect of these plans, in order to implement measures so that any services that can operate from the start of the school year at 50% capacity will do so and over the coming period all other post-primary transport services will be re-organised and additional services will be provided as required to allow for physical distancing. "
Arrangements made for primary school transport scheme will proceed as planned.
Over 120,000 children were brought to schools bu buses each day last year.