President Duterte has imposed strict military law on the Philippines
The controversial leader told soldiers in the country's south on Friday they were allowed to rape up to three women.
He said: "I will be imprisoned for you. If you rape three (women), I will say that I did it. But if you marry four, son of a whore you will be beaten up.”
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The comments come as Mr Duterte imposed 60 days of martial law after a group aligned with the so-called Islamic State (ISIS) launched raids on the city of Marawi.
But his supposed joke has prompted fierce criticism as activists claim soldiers may now believe they could commit rights abuses as they enforced martial law.
President Duterte is known for his controversial and shocking comments
Mr Duterte made the remark in a speech to soldiers on Mindanao island, in an area where martial law has been imposed.
He added: "If you go down, I go down. But for this martial law and the consequences of martial law and the ramifications of martial law, I and I alone would be responsible, just do your job, I will take care of the rest.”
Phelim Kine, a deputy director with Human Rights Watch's Asian division, described the joke as a "sickening attempt at humour".
Unseen photos of President of the Philippines, Rodrigo Duterte
Thu, December 29, 2016
The controversial presidency of the Philippines' leader Rodrigo Duterte.
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I will be imprisoned for you. If you rape three (women), I will say that I did it
President Rodrigo Duterte
Gabriela, a women's political party in the Philippines, added: "Rape is not a joke. Martial law and the heightened vulnerability to military abuse that it brings to women and children are not a joke either.”
While Chelsea Clinton, the daughter of ex-US president Bill Clinton and former secretary of state Hillary Clinton, tweeted: "Not funny. Ever.”
“Duterte is a murderous thug with no regard for human rights. It's important to keep pointing that out & that rape is never a joke."
President Duterte has prompted fierce criticism
Mr Duterte is well known for his controversial comments – and this is not the first time he has made a joke about rape.
In the lead-up to his presidential election win last year, the Philippines leader recalled a 1989 prison riot in which an Australian missionary was killed after inmates lined up to rape her.
The firebrand politician described the victim as beautiful, adding that as mayor of Davao city where the riot took place, he should have been first in line.
Mr Duterte later apologised for what he claimed was a joke and said he did not intend disrespect to women or rape victims.