Duterte's declaration "is just the latest in a series of misogynist, derogatory and demeaning statements he has made about women", Human Rights Watch said in a statement sent to Al Jazeera on Monday.
"It encourages state forces to commit sexual violence during armed conflict, which is a violation of international humanitarian law," Carlos Conde, a Human Rights Watch representative in the Philippines, said.
According to a government transcript of a speech he delivered on February 7, Duterte said Philippine soldiers should not kill women rebel fighters.
"We will just shoot your private parts, so that if there are no more private parts, you would be useless," Duterte said in his native Visayan, a language spoken in central and southern Philippines.
The president also chastised female soldiers for abandoning their children and families, in order to join the communist movement.
Emmi de Jesus, a Congress member representing the Gabriela Women's Party, denounced Duterte's "nasty remark", saying it contributes to the culture of "impunity" in the country.
De Jesus said the president "further confirms himself as the most dangerous macho-fascist in the government right now".
She added that Duterte is taking "state terrorism against women and the people to a whole new level", and pushing soldiers "to commit more bloody human rights violations and grave abuses of international humanitarian law".
Spokesperson: Duterte's jokes 'funny'
Duterte has been under fire several times for making misogynistic comments.
In January, during his visit to India, hetold a group of Indian and Filipino business leaders in New Delhi that he would like to attract visitors to the Philippines by offering"42 virgins".
In July 2017, he also made rape jokes while talking about Miss Universe.
Two months earlier, Duterte told soldiers fighting Muslim armed fighters in Marawi that they could rape up to three women without getting punished.
"I'll imprison you myself," he said, referring to soldiers who commit violations. Then he said: "If you had raped three, I will admit it, that's on me."
In the lead-up to his presidential election win in 2016, critics were outraged when he recalled a 1989 prison riot in which an Australian missionary was killed, and inmates had lined up to rape her.
Duterte said the victim was "beautiful" and as mayor of Davao City, where the riot took place, he should have been first in line. He later apologised and said he did not intend to disrespect women or rape victims.
On Wednesday, Harry Roque, Duterte's spokesperson, defended the president's string of sexist comments, saying critics should lighten up.
"You know, sometimes, these feminists are really a bit OA," Roque said using the Filipino term to mean over-acting.
"I mean, that's funny. Come on. Just laugh", he told a pro-Duterte social media personality, adding that people "identify with his humour".
The Duterte administration has been engaged in an on and off peace negotiations with the communist rebels in the Philippines, since he came into office in mid-2016.
But following new clashes between government forces and rebel fighters in 2017, Duterte signed a proclamation labelling the communist fighters as a "terrorist" group, essentially breaking off the peace process.
He has also ordered the arrest of several community leaders.
The Communist Party of the Philippines launched a rebellion in 1968 that has so far claimed the lives of more than 30 000 people.
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