Jeff Johnson said the province is also reviewing school employment contracts to make sure they don't infringe on human or charter rights.
"I'm very concerned," Johnson told reporters Monday.
"With all of our schools we expect that they'll be adhering to all provincial legislation, the Education Act, (and) the Alberta Human Rights Act.
"We need to look at all the school boards and find out who has these (provisions) in their policies."
His comments come after reports that the stated policy of Prairie Christian Academy near Calgary requires teachers to abstain from "homosexual relations" and not cheat on their spouses.
The school also warns students against illicit sexual conduct, and says the unjust will burn in hell's "lake of fire."
The academy receives public funding and is now getting $7 million from the province for building upgrades.
In Calgary, students and teachers at the publicly funded Heritage Christian Academy can be expelled or fired for engaging in a lifestyle of "sexual immorality" previously defined as including gay sex.
Opposition politicians say Johnson needs to act immediately.
"It's up to the education minister to make sure that no teacher or no student is at risk of being discriminated against that way," said Wildrose Leader Danielle Smith.
"It's an incorrect policy."
NDP Leader Brian Mason said, "We need to be really clear that you cannot discriminate in an educational institution or in any other institution on the basis of sexual orientation."
Liberal critic Kent Hehr says the government has to share the blame.
"If the government isn't already aware of what's been happening in many of our schools I'd be surprised," said Hehr.
"Either they have, as in past, condoned these principles, or they're turning a blind eye.
"This falls right in the minister's lap."
Last week, the plight of gays in schools made headlines when Hehr championed a motion urging the government to push schools to allow the formation of gay-straight alliances to help gay students avoid bullying.
The motion was defeated by a coalition of Progressive Conservatives and Wildrose members on the grounds it was an issue best left to school boards.
On Monday, Johnson said he'd talked to the two Christian academies, and said they told him they'd be willing to set up gay-straight alliances if the students called for them.
Hehr was skeptical.
"That's kind of rich when you look at the language in some of their (school) documents," he said.
"I'd like to see them put their money where their mouth is on that issue."