In a speech at a military camp on Friday aimed at lifting troops' spirits after he imposed martial law across the southern Philippines, Duterte told them they were allowed to rape up to three women.
"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," he said.
Duterte, who uses profanities regularly, also attracted controversy last year when during an election campaign speech he joked that he had wanted to rape a "beautiful" Australian missionary who had been murdered in a Philippine prison riot.
Clinton joined many people on social media on Saturday to criticise Duterte, who has also carried out a war on drugs that has left thousands of people dead and rights groups say may be a crime against humanity.
"Not funny. Ever," wrote the daughter of ex-US president Bill Clinton and former secretary of state Hillary Clinton on her verified 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."
Phelim Kine, a deputy director with Human Rights Watch's Asian division, described the joke as a "sickening attempt at humour".
"Duterte's pro-rape comments only confirm some of the worst fears of human rights activists that the Duterte government will not just turn a blind eye to possible military abuses in Mindanao, but may actively encourage them," Kine said.
Gabriela, a women's political party in the Philippines, also expressed outrage.
"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," it said in a statement.
Duterte's aides frequently explain away his most controversial comments as being "merely rhetoric" or an "exaggeration" or comments only ordinary Filipinos would appreciate.
His spokesman, Ernesto Abella, released such a statement on Saturday explaining that Duterte was using "heightened bravado" when trying to raise the morale of the troops.
"He gave his full support to the men and women in uniform, taking complete responsibility for their actions, even exaggeratedly describing crimes like taking a fourth wife," Abella said, while ignoring Duterte's preceding rape remark.