Australia's Human Rights Commissioner Tim Wilson has written to the Baird government expressing concern that the national school chaplaincy program could be detrimental to gay and lesbian students.

Mr Wilson's letter to NSW Education Minister Adrian Piccoli was written just days after the Gayby Baby furore erupted in Sydney.

"Chaplains may place their private spiritual views on [gay and lesbian] issues ahead of the wellbeing of young people they are charged to support": Tim Wilson.

Mr Piccoli issued a memo to schools asking them not to screen the film during class time on Wear It Purple day.

In the letter, Mr Wilson asks for a review to be conducted of complaints made about chaplains to assess whether inappropriate advice is being given to young gay and lesbian students.