Duterte is notorious for his foul-mouthed speeches that include insults, threats to perceived enemies and references to rape that he casts as jokes.
The latest unfiltered comments came during an appearance before the Filipino community in Tokyo last week.
During his speech Duterte appeared to say that one of his high-profile critics, Senator Antonio Trillanes, was gay.
"Trillanes and I are similar. But I cured myself," the president said.
The president explained that he "became a man again" after meeting his now ex-wife.
"So beautiful women cured me," he added.
Duterte has a wavering record when it comes to gay rights. During his campaign for president in 2016 he voiced support for same sex marriage, but later backtracked.
He has also used homosexuality as an insult, including against Philip Goldberg, then US ambassador to Manila.
Bahaghari, a gay and transgender advocacy group, said Duterte's comments were dangerous and retrograde.
"It is symptomatic of an even graver illness: one of ignorance, prejudice and hate," the group said in an statement.
"These statements, like his perverted and offensive comments on women, cannot be taken lightly or dismissed merely as jokes," the group added.
The World Health Organization and American Psychiatric Association consider homosexuality as a sexual orientation and not a disorder.
The Philippines has a reputation for openness toward homosexuality, but watchdogs warn legal protections are lacking.
At the same time, the Catholic Church is a powerful force in the nation where the majority of its 106 million people are counted as believers.
Abortion and divorce are both illegal, due in part to fierce resistance to change from the church.