Pacquiao, who is currently running for a seat in the Philippine senate, made the comments in an interview with a local TV network.
"It's common sense," he had told a local TV network.
"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 who is revered in the Philippines for winning world boxing titles in eight different weight classes during his 20-year career, attempted to apologise on Thursday via a video message on his Twitter account.
"I'm sorry for hurting people by comparing homosexuals to animals. Please forgive me for those I've hurt," Pacquiao said.
Same-sex marriage is not allowed in the Philippines, where more than 80 per cent of the 100 million population is Roman Catholic.
- AAP