Education Minister Norma Foley has said if parents wish to drive their children to school, instead of taking a school bus, they can be reimbursed.
She also denied there had been a u-turn on issues around school bus capacity.
She said the changing advice on school transport is due to the decisions from public health authorities.
Calling it a "huge logistical challenge", she told Newstalk Breakfast: "We will be offering the facility to parents who wish to do so - we will offer to them, if they can provide their own transport, we will recompense them for doing that if they are ticket holders on the bus".
"What we're saying is we will offer parents the facility to provide transport themselves, and we will recompense them for doing that".
"You will appreciate that initially, the public health advice suggested that students were viewed as a single cohort of passengers travelling in a controlled environment.
"And as such buses could operate as they always operated with additional measures like hand sanitiser, PPE for the bus driver, cleaning resources and all of that."
"Then subsequently two weeks ago there was further advice for our schools in terms of our second-level students wearing masks and staff doing likewise - and again, we've embraced that.
"And the latest advice which just came some time on Tuesday... is suggesting that school transport for primary school children will proceed as normal, and for second-level children - again where social distancing isn't possible - students will wear masks and that we should also look at rolling out capacity to the level of public transport.
"We have immediately engaged with Bus Éireann in that respect.
"We are doing that, and so on a rolling out basis the additional buses will be made available."
"In fairness the department has always worked hand-in-hand with public health and... everything that is in our roadmap is based on the basis of the best public health advice that was available at a given time.
"So it's not a question of a u-turn, it's a question of acknowledging the public health advice available at a given time."
On the resignation of her Cabinet colleague Dara Calleary, she said: "To be fair, Dara Callery has been unequivocal in his remorse for the situation that has arisen and absolutely unequivocal in making a genuine apology in relation to it and taking action.
"We all make mistakes, that's human nature, but he has put his hand up now and he has acknowledged that and he has expressed, as I say, genuine remorse for what has happened".