Pacquiao's comments have drawn widespread condemnation from gay Filipino celebrities, rights groups and netizens.
Pacquiao positions himself as a conservative Christian politician and is currently running for a senate seat in the country's May elections. He is a member of the Philippines house of representatives.
Speaking to local station TV5, the boxing champion tells interviewer "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."
Gay rights organization Ladlad issued a call for voters to boycott Pacquiao. In a statement to local media they said that his comments "betrays a shallow understanding of sexual orientation and gender identity," according to the BBC.
Local celebrities including Filipino comedian Vice Ganda and singer Aiza Seguerra also spoke out against Pacquiao's comments.
The Philippines catholic church remains very conservative on gay rights, as does much of the country. However the capital Manila boasts a vibrant gay scene.
Watch Pacquiao make the comments (in Tagalog) below: