The council and the union agree that most parents are paying the new charges, which were brought in this term. The EIS argues that pupils have failed to appear as planned because parents could not afford the charges.
But Margaret Dobie, senior education officer in the city, said that she had received no complaints from parents about being unable to pay.
Willie Hart, EIS local secretary, accepted that there was no evidence of pupils being excluded. But there are examples of enrolled pupils failing to appear, he said.
The grievance will be examined by the education directorate.