His claim comes months after he tried to detach himself from reports that he wanted to push a family planning policy.
Mr Duterte has previously said he thinks families should have a maximum of three children.
The politician has previously 'joked' that fathers of big families need to have their genitals amputated.
The Catholic Herald has reported that he said: "I will reinstall the program of family planning. Three's enough.
"I've also been colliding with the Church because it's no longer realistic."
As mayor of Davavo in the south of the country, he has also spoken about paying men to undergo sterilisation.
Speaking in May, Duterte said: "I cannot force the people to follow.
"We are just suggesting that you are in good hands if you just limit the number of your children."
In 2012, a law was passed requiring public health centres to give out free contraception and sex education was made compulsory in schools.
Duterte has also spoken about bringing back family planning after he heard one report that a mother had given birth to ten children.
"I am a Christian, but I am a realist and we have to do something about our population," he said.
The politician has previously had run-ins with the country's bishops over the death penalty and 'joked' about a Australian missionary who was raped and murdered in his town in 1989.
He has also called the pope names and said the Church is "hypocritical."
Duterte will be inaugurated on Thursday.
