Sam Galbraith, Children and Education Minister, said officials would be writing to authorities seeking suggestions about how co-ordination could be improved.
Mr Galbraith said in a statement: "I think it is important that education authorities work together to take a consistent approach. I know that such discussions are often standard practice but I have asked my officials to write to all athorities to remind them that co-operation when setting school dates is desirable wherever possible.
"I have also asked them to inform the Scottish Executive about the difficulties they face in carrying out this task."
Mr Galbraith acted following representations about the problems parents face when authorities set different dates. The difficulties surfaced following local government reorganisation which created a larger number of smaller councils with people living and working in different areas.