Critics say Rodrigo Duterte’s remarks can encourage sexual violence and war crimes.
Mr Duterte made his comment last week when addressing a group of former communist rebels.
“Tell the soldiers, ‘There’s a new order coming from the mayor. We won’t kill you. We will just shoot your vagina,'” he said, according to media reports.
“If there is no vagina, it would be useless,” Mr Duterte continued.
The left-wing group Karapatan, Alliance For The Advancement Of People’s Rights, said the President “has distinguished himself as a frothing-in-the-mouth fascist who incites the worst violations of international humanitarian law”.
Human Rights Watch said the remark is the latest in a “series of misogynist, derogatory and demeaning statements he has made about women” which encourage state forces to commit sexual violence during armed conflict.
Mr Duterte acknowledged that he has a “bad mouth” but added: “The problem here is that I won” the election.
Mr Duterte, who took over in 2006, has a history of controversial remarks, including calling Barack Obama “son of a whore” and bragging about killing people when he served as mayor of the city of Davao.
Human rights groups have also condemned his violent crackdown on drugs, in which thousands of people have been killed.