Joel Zeferino was speaking as the debate on terminations reignited in his country amid the spread of Zika which can lead to birth defects in babies.
"We understand this is an issue that needs to be discussed with society in a much more open and democratic manner," he said.
"We need to include in this debate the women who suffer these abortions, the women who live on the outskirts of our cities, the black women, these are the ones who, in fact, resort to illegal abortions."
Abortion is illegal in Brazil but calls are mounting on the government to change the law so females infected with the virus can have a termination.
The Zika outbreak is spreading rapidly across Latin America.
Elsewhere the Anglican Church has said it remains undecided on the issue whilst the Catholic Church has confirmed it remains prolife regardless of the virus.
Brazilian President Dilma Rousseff has met with members of the National Council of Christian Churches of Brazil to ask them to talk about Zika from the pulpit.
She wants to use churches to spread awareness about Zika.