The church and other contraception opponents filed petitions with the Supreme Court, which issued several rulings blocking parts of the law. The court continues to prevent the Health Department from procuring, distributing or selling birth control implants, a ban that women’s health groups fear could be extended to the pill and other forms of hormonal birth control when existing certifications expire in 2018.

Last year, Congress cut the Health Department’s budget for contraceptives, citing the court order halting the distribution of implants. Local agencies have administered the law differently in different districts, and sex education in particular has varied widely by school district. This month, Vicente Sotto III, the Senate majority leader, vowed to stop the distribution of condoms in high schools, arguing that they encouraged promiscuity.

The battle is not over, but Mr. Duterte’s order provides clear guidance to government agencies and local health officials that they should uphold the law, eliminating some of the ambiguity the various court decisions have caused. And while the church still opposes the law in principle, it has scaled back its public campaign against it. Two archbishops, in interviews, acknowledged defeat.

The Duterte administration says it can provide desperately needed services that are vital to lifting millions of people out of poverty. It estimates that there are six million women, two million of whom are poor, who do not have access to modern forms of contraception.

Mr. Duterte’s order aims to achieve “zero unmet need for family planning” by 2018, helping to meet his goal of reducing the poverty rate to 14 percent by the end of his administration in 2022, down from the 2015 level of 21.6 percent.

Sex education, advocates say, has been a failure. The Philippines is the only country in Asia where teenage pregnancy increased over the last two decades, according to the United Nations Population Fund.