Rodrigo Duterte is also calling for a three-child policy in the country.
The 70-year-old, who identifies as Christian but no longer Catholic, has often had fraught relations with the church in the Philippines, which has traditionally opposed contraception.
Mr Duterte said: "I only want three children for every family," according to The Times.
He went on: "I'm a Christian, but I'm also a realist so we have to do something [about] our over-population.
"I will defy the opinion or the belief of the Church."
It is not clear what form this policy or idea might take.
Mr Duterte remains well-supported in the overwhelmingly Catholic country, where 80% of people identity as believers.
He has made headlines around the world following a number of controversial comments about bishops, as well as Pope Francis and a 'joke' about a raped and murdered Christian missionary from Australia.
In one of his most recent interviews, he said the Catholic Church was "the most hypocritical institution" and it was not relevant.
Days before the election, a letter was released by Catholic bishops in the country urged votes to steer away from the "morally reprehensible" Mr Duterte.
A spokesperson for the bishops conference said that it would always defend the Church's teachings.
