Secondary principals say many year 10 students did not come to school on Thursday despite the suspension of a teachers' strike affecting them.
The Post Primary Teachers' Association called off the action on Wednesday afternoon so pay talks with the Ministry of Education could resume.
But Secondary Principals Association head Patrick Walsh says schools were not notified until 3.15pm - after most students had left for the day.
Mr Walsh says any decision to halt the strike should have been made about midday so schools had time to tell students.
Earlier on Thursday, Education Minister Anne Tolley said teachers pushing for pay increases needed to accept reality.
Sticking points in the talks have included class size and teaching conditions.
Both sides say the negotiations are the last chance to reach a settlement before the end of the school year.
Ms Tolley says she is pleased the talks are back on because strikes are very disruptive for parents and students.
She says she has made it very clear to teachers that there is not a lot of money to go round.