Prime Minister Malcolm Turnbull has ordered a review into a controversial school education program aimed at promoting acceptance of gay, lesbian, bisexual and transgender (LGBTI) students.

The move was immediately hailed by the Australian Christian Lobby (ACL) as a win against "rainbow ideology," while Labor and the teacher's union slammed Mr Turnbull for buckling to the conservative wing of the Liberal Party.

The Safe Schools teaching manual, set up by Labor but launched by the Coalition in 2014, has been under fire in recent weeks from conservative politicians, the ACL and News Corp newspapers.

An independent review announced on Tuesday will advise Education Minister Simon Birmingham on whether the program's material is "age appropriate" by mid-March.