"I'm sorry for comparing homosexuals to animals. Please forgive me for those I've hurt," Pacquiao said in a video post on Instagram, his arms crossed on Tuesday.
Pacquiao said he was not condemning homosexuals but was standing by his conservative Christian faith. AFP reports.
"I love you all with the love of the Lord. I am praying for you."
Pacquiao told television station TV5 earlier this week: "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."
Gay marriage is outlawed in the Philippines due to strong opposition from the Catholic Church and 80 percent of the country's 100 million people subscribe to the faith.
Gay marriages are officiated at small churches but are not recognised by the mainstream church or the state.
The country's most popular gay comedian, Vice Ganda, posted #PrayForMannyPacquiao to his 6.7 million followers on Twitter as he tore into the boxer.
"Some people think they can judge people, like God, just because they've attended a prayer meeting and read the Bible," he said.
"The Senate needs experts on politics and law, not blind prophets," Vice Ganda added.
Singer Aiza Seguerra, who recently married her actress-girlfriend, called on voters to boycott Pacquiao, who is also preparing for his last boxing fight in April, calling him an "ignorant, bigoted hypocrite".
"You might have done our country proud but with your statement, you just showed the whole country why we shouldn't vote for you," Seguerra said in a post on Instagram.
Pacquiao gave the television interview as part of his campaign for one of 12 seats in the nationally-elected senate.
The most recent surveys suggest he would win.
He currently represents his wife's impoverished home province of Sarangani in the House of Representatives but is notorious for his chronic absences, favouring boxing training over legislation.
In one of the rare times he spoke at the legislature, Pacquiao quoted heavily from the Bible as he vigorously contested a proposed law, since passed, granting free condoms to the poor.
He credits his renewed Christian faith for transforming him from a free-spending womaniser and gambler into a devoted family man who can recite Bible verses.
"Outside the boxing ring, I don't think Manny Pacquiao should be taken seriously. It struck me first as funny. I pity him," Kakay Pamaran, a pastor at one of Manila's gay churches, told AFP.
"I would advise him to talk to more LGBT (lesbian gay bisexual and transgender) persons, meet them and not just reduce his concept of LGBT to the sexual act."