Sister Lucia Caram of the Dominican order made the comments on Spanish television on Sunday.
"I think Mary was in love with Joseph and that they were in a normal couple - and having sex is a normal thing," she told the Chester in Love show.
"It's hard to believe and hard to take in. We've ended up with the rules we invented without getting to the true message."
Angry viewers then started an online petition to have her suspended from the order.
Bishop Romà Casanova Casanova of Vic also condemned her comments, writing in a statement:
"The belief that Mary was a perpetual virgin forms part of the faith of Church from its beginnings and that this truth of faith was collected and proclaimed by the Second Council of Constantinople, being the primary Marian dogma observed by Catholic and Orthodox Christians. Such statements do not conform to the faith of the Church."
After the angry backlash Sister Lucia apologised to anyone who felt offended, but said she was worried by the "fragmented, ideological and perverse" way in which her remarks had been construed.
She added that "some heretic-bashers, thirsting for vengeance and driven by hatred" had lied about her and made "serious threats, including to my life".