MANILA (AFP) - Catholic bishops on Sunday (Nov 5) led thousands of Philippine worshippers in calling for an end to killings in President Rodrigo Duterte's drug war as they urged police and troops to stop the violence.

The killing of three teenagers in August triggered rare public protests against Mr Duterte's anti-drugs campaign, with rights groups accusing him of committing crimes against humanity in a crackdown that has claimed thousands of lives.

The Catholic Church, which counts 80 per cent of Filipinos as followers, has been one of the leading critics of the war on drugs and has launched campaigns to stop the killings, including one starting on Sunday dubbed "Heal Our Land".

The church organised a mass and procession along a historic Manila highway called EDSA, where a bloodless popular revolt ended the iron rule of dictator Ferdinand Marcos in 1986.

About 3,000 people - including opposition lawmakers, students and church groups - joined the event, according to police. They carried candles and placards reading, "Stop the Killings. Start the Healing".

"Peace to you in the armed forces and the police. Stop the violence and uphold the law," Archbishop Socrates Villegas, the president of the Catholic Bishops' Conference of the Philippines, said at the mass.

"If we do not stop the killings, there will be a punishment for a nation that kills its own people."

Mr Duterte, 72, won elections last year after campaigning on a law-and-order platform and since then, police have reported killing more than 3,900 "drug personalities".

The President's spokesman on Sunday said he did not condone extrajudicial killings, adding the government was investigating another 2,243 deaths in unsolved "drug-related" cases.

"The president himself made a clear stance that any violation committed by the police during operations would be dealt with accordingly," Mr Harry Roque said.

Critics say that Mr Duterte's frequent public pronouncements on the drug war have been direct incitements to kill.

Archbishop Villegas said the killings tested the nation and cited the case of 17-year-old student Kian Delos Santos, who died in a police anti-drug raid in August.

"Please stop. I still have a test tomorrow," he quoted Delos Santos as saying following witness accounts that he had begged for his life.