The Christian was accused of making a homophobic slur, he said homosexuals as "worse than animals" in a television interview.
He said: "It's common sense. Do you see animals mating with the same sex?''
"Animals are better because they can distinguish male from female.
"If men mate with men and women mate with women they are worse than animals," Pacquiao said when his comments were translated into English by TV5's Facebook page.
Fr Jerome Secillano, from the Catholic Bishops Conference of the Philippines (CBCP), said that Pacquiao was simply quoting the Bible.
According to Gay Star News Fr Jerome Secillano, during an interview with dzMM radio station, said: "This is really in the Bible.
"There is this quote he (Pacquiao) uses from the Bible and we cannot change that."
He did comment though that the boxer should not have used offensive language.
Manny Pacquiao, who is running for political office in the Philippines, has apologised for his comments.
Sponsor Nike dropped him as one of their sponsors after saying his comments were "abhorrent."
A Nike spokesperson said in a statement to Press Association Sport: "We find Manny Pacquiao's comments abhorrent. Nike strongly opposes discrimination of any kind and has a long history of supporting and standing up for the rights of the LGBT community.
"We no longer have a relationship with Manny Pacquiao."