His remarks were condemned across the world - including by gay basketball star Jason Collins and the boxer who defeated him last May, Floyd Mayweather.
Mr Pacquiao then apologised on Facebook, saying he was sorry for hurting people and was "not condemning LGBT" but was still against gay marriage.
But yesterday, a Bible quote appeared on his Instagram account, reading: "If a man has sexual relations with a man as one does with a woman, both of them have done what is detestable. They are to be put to death; their blood will be on their own heads."
Local Filipino media captured a screenshot of the image before it was deleted and Mr Pacquiao's staff in General Santos confirmed that the post had been published on the boxer's account.
However, Mr Pacquiao - still wearing his Nike sports gear - insisted the row had not affected him.
"I'm happy. I'm always happy because God is with me," he said.
Mr Pacquiao intends to retire from boxing after his April fight against Timothy Bradley from the US, and will step up his career in politics.
The boxer, who has converted from Catholicism to an evangelical Protestant faith, has said he wants to be president.
Homosexuality is not a crime in the Philippines, but gay marriage is against the law in the strongly Catholic country.
-AP
