Rodrigo Duterte, who is to be sworn to the presidency on Thursday, said having many children has driven families deeper into poverty, and he reiterated his recommendation for Filipinos to have three at most.
Known for his profanity-laden speeches, Duterte jokingly threatened to have penises of defiant men chopped off and cited his family planning programme as a longtime mayor in southern Davao city, where he has offered cash rewards to villagers who volunteer to undergo free vasectomy or ligation and to doctors who perform the procedures.
"I will reinstall family planning. Three's enough," Duterte said in a speech after a flag-raising ceremony in front of the Davao city hall.
"I've also been colliding with the church because it's no longer realistic."
It was not clear if Duterte would replicate the reward system nationwide.
Duterte praised former President Fidel Ramos, who backed his presidential candidacy, for courageously promoting contraceptives as the country's first Protestant leader starting in 1992.
Duterte's predecessor, Benigno Aquino III, also figured in a high-profile spat with the Catholic church for signing a 2012 reproductive health law that allowed the government to finance the acquisition and distribution of contraceptives after overcoming a legal challenge by opponents.
Many politicians have tried to avoid colliding with influential Catholic bishops in the Philippines in the past by taking a vague position or not aggressively advocating contraceptives use.
Catholic leaders considered the law an attack on the church's core values. Aquino's government said it helped the poor manage their number of children in a country that has one of Asia's fastest-growing populations.
Duterte has had an adversarial relation with the church. During the campaign, Duterte had a tiff with Catholic bishops after cursing Pope Francis due to a monstrous traffic jam during the papal visit in January last year.
Last month, Duterte blasted the local Catholic church as "the most hypocritical institution" and accused some of its bishops of asking for favors from politicians.