Police outnumbered the less than 50 protesters at the pro-family religious group event, letting attendees in through a police line guarding the entrance.
One protester got inside, scaled the stage and positioned herself in front of Christian lobbyist and NSW MP Fred Nile, splashing fake blood on her white suit in a pro-choice stunt.
"We don't want your backyard abortions," Phaedra Press, from the Whistleblowers, Activists and Citizens Alliance, said, before security ejected her.
Federal Social Services Minister Kevin Andrews and Victorian Attorney-General Robert Clark were due to give speeches at the Saturday event.
But both cancelled their appearance on Friday, because the evangelical Christian group Catch The Fire Ministries was hosting it.
Conference convener Babette Francis denied the protesters disrupted the event, saying more people than expected attended.
"If we thought they'd be quiet, we'd be happy to let them in.
They could listen to the talks and ask and maybe learn something or agree to disagree," she said.
"It's silly what (the demonstrators) are doing. I think it's a waste of time and energy.
"They're entitled to do that I suppose if they obey the police instructions."
Ms Francis said she was disappointed the government ministers cancelled.
Two arrests were made but despite some scuffles the demonstration appeared mostly peaceful.
Debbie Brennan, from the Coalition to Beat Back the Far Right, declared the protest a success after three venues refused to host the congress.
"When we saw that they were reduced out of desperation to finally hold their event in this isolated outskirts industrial area, of outer Melbourne, at Catch the Fire Ministries, we knew we had won," Ms Brennan told AAP.
"Then when we knew that all the parliamentarians had bailed out, we knew we had really won."
The conference drew criticism because of its stance against gay marriage, and claims of a link between breast cancer and abortion.
Ms Brennan said Mr Andrews and Mr Clark's excuse not to attend because Catch The Fire Ministries was hosting it was an excuse, given it was already sponsoring the event.
