Duterte said he has plans to reduce the number of unwanted pregnancies among the poor in the strict Catholic country.
The Roman Catholic Church has signalled it will campaign against his proposals which are likely to be challenged in the Supreme Court.
Currently contraception is available in The Philippines but at a high cost. Duterte's plan would mean poor woman would be able to obtain condoms and the pill for free.
Church officials say contraception is unbiblical but the government stresses steps are needed to cut poverty in the country.
Contraception is "pro-life, pro-women, pro-children, and pro-economic development", said Economic Planning Secretary Ernesto Pernia.
Duterte will pass the free contraception bill through an executive order, which means it does not need any further approval from other politicians.
It's the latest swipe at the Catholic Church in an ongoing row between the institution and the president.
