Mr Naughten was commenting on an announcement by the Department of Education today which confirmed that school buses will operate as normal because they differ from public transport.
School buses will carry the same number of students as normal, but children over 13 will have to wear masks and and all children will be given designated seats.
No advice
Mr Naughten says operators outside Bus Éireann's remit are not being given proper guidance.
"Private bus contractors that are operating outside of the school transport system have been given absolutely no advice, guidance or assistance in relation to how children are going to be transported to school. We could have a very serious outbreak if people are not made aware of the steps that need to be taken in transporting children to and from school."
The Labour Party's Education Spokesperson, Aodhán Ó Ríordáin also criticised the announcement today.
“I am very concerned by the way this announcement was made. Yet again we have a statement from the Department, this time in the form of a letter to parents with no ministerial follow up," Mr Ó Ríordáin said.
"There are a number of questions that Minister Foley needs to address. Is this now official Department of Education policy that school buses are exempt from social distancing requirements?"
He said the logical solution would be to acquire more buses to facilitate social distancing. He also asked why the Minister of Education did not attempt to make contact with Bus Éireann, the Department of Transport or the National Transport Authority about the matter.
Mr Ó Ríordáin also said there are other concerns that the Education Minister has failed to consider.
"She (Norma Foley) needs to outline how children with underlying conditions who avail of school transport will be accommodated because the letter sent from her Department effectively endorses putting them on packed school buses."