Minister for Education Richard Bruton has described the ASTI's non-co-operation with the new forms of student assessment in the Junior Cert as "extremely unfortunate".
Mr Bruton, who is before the Joint Committee on Education and Skills, said he would continue to work with the Association of Secondary Teachers in Ireland and the policy is one that should be implemented.
He said the Department has invited the union to adopt the English element of the curriculum so children examined in June will not be "handicapped".
Fianna Fáil TD Thomas Byrne asked Mr Bruton if he could guarantee that students in ASTI schools would not lose marks.
The Minister said he could not make that guarantee.
In a statement issued this morning, Mr Byrne said that children in ASTI schools are facing punishment in their State examinations due to matters outside their control.
"The Government should not be using students' grades as a bargaining chip with unions. We cannot allow a situation to develop where children are penalised as a result of this industrial dispute.
"The minister needs to change his attitude on this immediately," Mr Byrne added.