For years the bodies piled up.

Some were shot by vigilantes on motorbikes. Others had bullets in the head, execution style. In killing after killing, the police would only describe the victims as “drug suspects” who had resisted arrest, a charge that rarely stood up to even minor scrutiny. And yet the slaughter continued with impunity, at the behest of the man who was elected president of the Philippines, Rodrigo Duterte.

But on Tuesday, nearly three years after Mr. Duterte left office, a major step was taken toward accountability for thousands of Filipinos who have long sought justice for their loved ones. Acting on a warrant issued by the International Criminal Court, which had been investigating Mr. Duterte’s antidrug campaign, the Philippine authorities arrested Mr. Duterte at Manila’s main airport as he returned from a trip to Hong Kong. On Tuesday night, he was flown out on a plane that was bound for The Hague, where the court is based, according to two people with knowledge of the matter.

The I.C.C. accused Mr. Duterte, 79, of crimes against humanity during his time as president and when he was the mayor of the city of Davao. His case will be a high-profile test of the court, which in recent months has sought the arrest of Israel’s prime minister, Benjamin Netanyahu, and the head of the military junta in Myanmar, Min Aung Hlaing, on the same charges as Mr. Duterte. But those orders are unlikely to come to fruition, much like the court’s warrant for President Vladimir V. Putin of Russia that was issued two years ago.

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A victim of unidentified gunmen on motorcycles in Manila, in 2016. Rights group say about 30,000 people were killed in Mr. Duterte’s drug war. Credit…Daniel Berehulak for The New York Times

Mr. Duterte’s camp said his detention was illegal, arguing in part that the I.C.C. had no jurisdiction in the Philippines because he had withdrawn the country from the court when he was president. But in the warrant, a three-judge panel wrote that it was investigating killings during the time the Philippines was still a member of the court. And the nation remains a member of Interpol, which can seek arrests on behalf of the I.C.C. A representative of Interpol was present when Mr. Duterte was arrested.

Mr. Duterte’s arrest pierced the culture of impunity he had built around his so-called death squads. Even after his single, six-year term ended, he seemed to be above justice. His successor, Ferdinand R. Marcos Jr., rose to the presidency after forming a political alliance with Mr. Duterte’s daughter, Sara, who became vice president. Early in his administration, Mr. Marcos indicated that he would not cooperate with the I.C.C.

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