The 37-year-old, who is running for a seat in the country's senate, made the remarks on a television program broadcast by Filipino station TV5.
Campaigning to secure one of 12 national seats he said: "It's common sense. Will you see any animals where male is to male and female is to female?
"The animals are better. They know how to distinguish male from female. If we approve [of] male on male, female on female, then man is worse than animals."
He first clarified his comments on his Instragram page, before later posting a video message on his Twitter account.
"I'm sorry for everyone who got hurt due to my comparison of gay people (homosexuals) to animals," he said. "It was my mistake. Please forgive me for those who I've hurt.
"But this does not change my position against same sex marriage. That's what I believe. My only mistake is comparing gay people to animals."
The first fighter to win world titles at eight different weight divisions, Pacquiao is set to retire after his bout with Timothy Bradley in April.
The Filipino boxer's "super fight" in Las Vegas with Floyd Mayweather
last year was the most lucrative in boxing history. Pacquiao lost a unanimous points decision.
Pacquiao currently sits in the Philippines' House of Representatives but is often absent due to his boxing commitments.
Reaction to his comments was swift, with one of the country's most popular gay comedians, Vice Ganda, using the hashtag #PrayForMannyPacquiao on Twitter.
"The LGBT is a group of people," Ganda told his 6.7 million followers. "We are humans. But not animals. Though we're no saints we will pray for Manny Pacquiao."
Pacquiao responded to the criticism on Instagram account, prior to posting a video of him back in training.
"I rather obey the Lord's command than obeying the desires of the flesh," wrote the boxer. "I'm not condemning anyone, but I'm just telling the truth of what the Bible says. The truth from the Bible is what changed me from my old ways."
Quoting from 1 Corinthians 6:9, Pacquiao added: "Or do you not know that wrongdoers will not inherit the kingdom of God? Do not be deceived: Neither the sexually immoral nor idolaters nor adulterers nor men who have sex with men."
He signed off by saying: "God Bless everyone I love you all."
Several hours after that, an apology was posted on the boxer's Twitter page.
The Philippines is Asia's most Catholic nation with 70 million devotees. Though gay marriages do take place, they are not recognized by the state or by the church.
Ladlad, an LGBT political organization, was also quick to condemn Pacquiao's comments.
"Rep. Pacquiao ... betrays a shallow understanding of sexual orientation and gender identity, nay, even the very basics of science," it said in a post on its Facebook page.
"His advisers—and Rep. Pacquiao himself—should bone up on LGBT issues that are becoming more important as the 21st century unfolds.
"Otherwise, they would be left behind in the Dark Ages, when the cavemen ruled, and the numbskulls roamed the earth."
Editor's Note: CNN's Leezel Tanglao contributed to this report