The Philippines' controversial President Duterte is on a collision course with the Catholic Church after he ordered millions of free condoms to be handed out.

The push to reduce unwanted pregnancies, particularly among the poor, is part of the government's plan to improve welfare among some of the country's poorest communities.

Duterte's economic planning secretary Ernesto Pernia said the push for "zero unmet need for family planning" was crucial to cut poverty.

He said the contraceptive plan was "pro-life, pro-women, pro-children, and pro-economic development", according to the BBC.

The Philippines' 103 million population is estimated to be 80 per cent Roman Catholic, according to the Pew Research Center.

The Church does not allow the use of condoms as a means of birth control and says abstinence and monogamy in heterosexual marriage is the best way to stop the spread of AIDS.

The row over condoms in the Philippines comes at a time when the Pope faces an extraordinary threat to his authority by an ancient Catholic order over contraceptive provision.

The Knights of Malta has refused to cooperate with a Vatican investigation, ordered by Pope Francis, in the latest twist of a public spat between two of the world's oldest institutions.

All members of the ancient Roman Catholic order, which now runs charities, hospitals and disaster relief in 120 countries, swear allegiance to the Pope.

However, its leaders have been locked in a legal tussle with the Holy See since one of its top knights was sacked.

Grand Master Matthew Festing fired Grand Chancellor Albrecht Freiherr von Boeselager, accusing him of allowing the use of condoms in Myanmar when he ran Malteser International, the Order's humanitarian aid agency.

Pope Francis effectively came to von Boeselager's defence, urging dialogue to resolve the internal dispute and appointing a five-member committee to investigate the circumstances of his December 6 ousting.

The Order, which last month told the Pope the incident was an internal affair, raised the stakes late on Tuesday with a bold statement rejecting the Vatican investigation as illegitimate.

"Considering the legal irrelevance of this group and of its findings relating to the legal structure of the Order of Malta, the Order has decided that it should not cooperate with it," a statement on its website said.

It also instructed members not to "directly or indirectly" contradict the official position if they talk to Vatican investigators.

Von Boeselager said in a statement that he "felt bound by the teachings of the Church".

He said he shut down two projects in Myanmar when he discovered condoms were being distributed but kept a third running for a period because closing it would have abruptly ended all basic medical services to poor people.

The Order's chaplain is Cardinal Raymond Leo Burke, an American whom the Pope demoted from a senior Vatican position in 2014 and who has been a leading conservative critic of the pontiff. Burke backed the sacking of von Boeselager.

The Order, which was formed in the 11th century to provide protection and medical care for Christian pilgrims to the Holy Land, has the status of a sovereign entity.

It has extraterritorial rights in Rome and maintains diplomatic relations with more than 100 states and the European Union and permanent observer status at the United Nations.

The Order has offices in central Rome and a large palace on the Aventine Hill overlooking the Tiber River with a breathtaking view of the dome of St. Peter's Basilica in the Vatican, which is a sovereign state.

Both the Order and the Vatican have their own car license plates and print their own stamps.

Additional reporting by Reuters.