The Education Ministry said on Tuesday that all teachers should make sure that morning prayers are said at school.
Pupils who do not wish to participate must sit quietly and show respect to the others, it added.
The ministry’s statement followed a report that pupils and parents of a primary school in Larnaca had protested because a sixth form teacher prohibited morning prayers, telling pupils that there is no God.
According to the news report on OMEGA Live, the school management has assured parents that the issue has been resolved, however no prayers are said in the specific class.
The president of the Primary School Teachers Union Philios Phylactou told philenews that the regulations on public primary schools were clear.
Under article 38, paragraph 10 notes before the start of the first period of class, teachers must make sure that morning prayers are said with those children who have class at that specific time.
Children who are not Orthodox Christian are allowed not to say prayers and not to cross themselves and to pray silently to their own God, he said.
This is covered in the 2017 regulations following the unanimous decision of the Education Ministry, POED and parents associations, Phylactou added.