Duterte on Friday told soldiers they could rape up to three women, in a speech aimed at reassuring them of his full support as they enforced his newly imposed martial law on the south of the Philippines.
"Not funny. Ever," wrote the daughter of ex-US president Bill Clinton and former secretary of state Hillary Clinton on her Twitter account.
In a second post she wrote: "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."
At the end of a long speech to naval officers and their families on Wednesday, Duterte said he was just being sarcastic as he took aim at people who criticised his rape remarks but particularly Clinton.
"These whores, they hear 'rape'. Like, like Chelsea, she slammed me. I was not joking, I was being sarcastic. Listen to the speech. I do not laugh at my own jokes," said Duterte, 72.
"I will tell her, when your father, the president of the United States, was screwing Lewinsky and the girls in the White House, how did you feel? Did you slam your father?"
Duterte was referring to Bill Clinton's acknowledged affair with a White House intern, Monica Lewinsky.
Duterte then accused American soldiers of raping women in the Philippines and Japan, without giving details, before returning to Clinton.
"I repeat, when president Clinton was fucking Lewinsky, what was your statement or your reaction?"
Duterte, who uses profanities regularly, also attracted controversy last year when during an election campaign speech he said he had wanted to rape a "beautiful" Australian missionary who had been murdered in a Philippine prison riot.
The Australian and American ambassadors to Manila voiced their disapproval at those comments, but Duterte reacted furiously then while insisting he had been taken out of context.
Duterte also frequently launches obscenity-filled tirades against critics of his drug war, which has seen thousands of people killed and led to warnings from rights groups that he may be orchestrating a crime against humanity.
Duterte last year called then US president Barack Obama a "son of a whore" for criticising the drug war.
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