Duterte has made numerous misogynistic comments since becoming president in June 2016.
Duterte said he already instructed Environment Secretary Roy Cimatu to clean up the tourist destination in six months.
President Rodrigo Duterte made the statement following reports that 11 of the 180 establishments inventoried by the DENR have incomplete sewerage systems and that their waste materials go straight to the drainage canal.
"Tell the soldiers. 'There's a new order coming from the mayor".
"Duterte (sic) latest nasty remark openly encourages violence against women, contributes to the impunity on such, and further confirms himself as the most risky macho-fascist in the government right now", said a representative for Gabriela, a feminist organization, in a statement. "Clean the g***** thing, '" the President said.
"He is pushing the fascist AFP to commit more bloody human rights violations and grave abuses of worldwide humanitarian law, and takes state terrorism against women and the people to a whole new level", the group said.
This is not the first time that Duterte has come under the limelight for being openly misogynistic and tried to brush it away "as a joke".
In January, during his visit to India, he told 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". Last summer, his rape joke about Miss Universe was widely condemned. 'I'll give you six months.
"I'll imprison you myself", he said, referring to soldiers who commit violations.
In the run-up to the presidential election, Duterte had impudently said that he, as mayor of Davao, "should have been first" to rape an Australian missionary in jail in 1989.
In a speech during The Manila Times 7th Business Forum here at Marco Polo Hotel late Friday, Duterte described Boracay as "cesspool" because of the perennial environmental problems plaguing the island.
On Wednesday, Harry Roque, Duterte's spokesman, defended the president's string of sexist comments, saying critics should lighten up. "If you marry four, you will get clobbered", he said.
Rodrigo Duterte told Philippine soldiers to shoot female rebels in their vaginas.
The Communist Party of the Philippines launched a rebellion in 1968 that has so far claimed the lives of more than 30,000 people.