Same sex marriage is legal in the giant nation following a federal court ruling earlier this year, and same sex partnerships have been legally recognized since 2004.
But the commission, headed by evangelical pastor Marco Feliciano of the Social Christian Party, adopted a measure to allow the Church to reject those "who violate its values, doctrines and beliefs."
"The proposal wishes to avoid priests being penalized if they refuse to carry out marriages, baptisms and other ceremonies between homosexuals or their children," the parliamentary news service reported.
The proposal outraged Socialist lawmaker Chico Alencar, who stormed: "This means the decriminalization of homophobia in churches. It harks back to the crusades; it is unconstitutional."
Brazil's constitution and justice commission will now assess if the proposal can go forward to full parliamentary and senate debate.
The commission triggered controversy earlier this year when it authorized psychologists to offer treatments designed to "cure" homosexuality as a disorder.
The proposal was shelved amid a storm of public protest.