Craig Campbell was told his views on same-sex relationships were incompatible with the ethos of South Coast Baptist College near Perth in Western Australia.
It is understood Mr Campbell, who attended the college as student, told senior colleagues about his relationship after posting what was described as a "suggestive" picture on social media.
Principal Des Mitchell was quoted by the Western Australian newspaper as saying: "The image he posted created interest in his personal life, including his sexuality.
"I shared with him that, at present, there is an inconsistency with his beliefs on sexuality and the college's beliefs."
Mr Campbell said his struggle to keep his boyfriend a secret from the college was made more difficult when three pupils arrived at the wedding of his aunt.
He told the gay and lesbian website, Out in Perth: "I told them [colleagues] I was in a relationship, and obviously this is something that I believe is fine from both a moral and a theological standpoint".
Mr Campbell also said hiding his same-sex relationship contradicted with his desire to instill values like honesty in his pupils and to see them live their own lives free of discrimination.
Disagreement exists in Australia over whether exemptions afforded religious organisations under Western Australia's anti-discrimination laws should be removed.