Prentice says Bill 202 is not one that lends itself to members being told how to vote.
The private member's bill, introduced by the Liberals, directs schools to allow students to set up the alliances if they so wish.
The alliances are support networks that give support to gay students and prevent them from being bullied.
Advocates say the alliances have been proven to reduce suicide among gay youth.
The NDP plans to support the bill while the Wildrose party says it wants to see changes to allow faith-based schools to opt out but still provide a safe atmosphere for all students.