Reverend Ouyang Wen Feng, an ethnic Chinese Malaysian ordained in the United States, announced last week that he would set up the church by 2010, prompting Malaysia's tourism minister to say the government would block the plan.
"We are going to set up a church just like any other one but the only difference is that we affirm and welcome those who openly declare themselves gays, lesbians or homosexuals," Ouyang told AFP Thursday.
"We will follow all the rules by applying all the proper licences. We already have a church of such stature in Singapore and I do not see why we cannot set up one here," he added.
Tourism Minister Adnan Tengku Mansor told AFP last week that Muslim-majority Malaysia was not keen on the church as they wanted the country to be seen as a "family-oriented" holiday spot.
Homosexuality falls under a Malaysian law prohibiting sodomy, which is punishable by up to 20 years in prison and whipping.