A plane carrying former Filipino president Rodrigo Duterte left the Philippine capital bound for The Hague on Tuesday following his arrest on an International Criminal Court (ICC) warrant stemming from his deadly crackdown on drugs, Manila said.

The 79-year-old faces a charge of "the crime against humanity of murder", according to the ICC, for a crackdown that rights groups estimate killed tens of thousands of mostly poor men, often without proof they were linked to drugs.

President Ferdinand Marcos Junior told a press briefing that the plane carrying his predecessor had departed at 11:03 pm (1503 GMT).

"The plane is en route to The Hague in the Netherlands allowing the former president to face charges of crimes against humanity in relation to his bloody war on drugs," said Marcos.

Duterte was arrested at Manila's international airport Tuesday after "Interpol Manila received the official copy of the warrant of the arrest from the ICC", the presidential palace said.

His daughter, current Vice President Sara Duterte, said he was being "forcibly taken to The Hague".

"This is not justice – this is oppression and persecution," she said in a statement.

Duterte had earlier taken to social media to say he believed the Philippine Supreme Court would step in and prevent his transfer.

"The Supreme Court will not agree to that. We do not have an extradition treaty," he said on Instagram live after his lawyers filed a petition.

An ICC spokesman confirmed the arrest warrant on Tuesday and said an initial appearance hearing would be scheduled when Duterte was in court custody. (AFP)