The International Criminal Court (ICC) has ordered an investigation of Philippine President Rodrigo R. Duterte’s crackdown on illegal drugs that has killed thousands, as it found “reasonable basis” that crimes against humanity had been committed.

In a statement, the Hague-based tribunal’s pre-trial chamber said the government’s anti-narcotic drive “cannot be seen as a legitimate law enforcement operation, and the killings neither as legitimate nor as mere excesses in an otherwise legitimate operation.”

The court said its judges considered evidence presented on behalf of more than 200 victims, and found that a “widespread and systematic attack against the civilian population took place pursuant to or in furtherance of a state policy.”

The court will also probe vigilante-style killings in Davao City when Mr. Duterte was still its vice mayor and mayor. The tough-talking leader, who is barred by law from running for reelection, has less than a year before his six-year term ends.

Former ICC prosecutor Fatou Bensouda sought the investigation before she retired in June, alleging that “state actors, primarily members of the Philippine security forces, killed thousands of suspected drug users and other civilians during official law enforcement operations.”

Philippine-based human rights group Karapatan said the ICC pre-trial chamber’s view that the attacks were widespread and systematic reaffirms the views of victims and their families.

“Duterte and his cohorts should be made accountable for these crimes,” it said in an e-mailed statement.

Presidential spokesman Herminio L. Roque, Jr., had said the Philippines would not cooperate with the ICC probe because it lost jurisdiction of the case after the country broke ties with the tribunal in 2019.

In June, Mr. Duterte said his government would not give full access to records of its war against illegal drugs and insurgency, citing national security concerns.

The ICC has said the withdrawal would not affect its investigation.

Tens of thousands of drug suspects have died in police anti-drug operations, many of them allegedly killed after resisting arrest, according to the United Nations.

In 2018, Mr. Duterte said extrajudicial murders happened under his administration’s drug war. The Philippine Commission on Human Rights has said the state was violating human rights for failing to stop police abuse.

At least 122 children were killed in the government’s deadly drug war between July 2016 and December 2019, according to the World Organization Against Torture.

Judges Peter Kovacs, Reine Adelaide Sophie Alapini-Gansou and Maria del Socorro Flores Liera signed the ICC order to investigate. — Kyle Aristophere T. Atienza