Since taking office two months ago, Duterte has begun making good on an election pledge to kill tens of thousands of suspected criminals, prompting criticism from rights groups who accuse him of inciting vigilante murders.
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He has also lashed out at the United Nations and described the US ambassador to Manila as a "son of a whore."
However, the White House said Obama would meet the firebrand leader on the sidelines of a summit in Laos, which begins on September 6, with the US president likely to voice disquiet over the bloodshed and Duterte's abusive remarks.
"We absolutely expect that the president will raise concerns about some of the recent statements from the president of the Philippines," Obama aide Ben Rhodes told reporters in Washington on Monday.
"We regularly meet with the leaders of our treaty allies where we have differences, whether it relates to human rights practices or derogatory comments. We take the opportunity of those meetings to raise those issues directly."
Duterte's war on crime has seen unknown assailants kill more than half the victims, according to police statistics, raising fears that security forces and hired assassins are shooting dead anyone suspected of being involved in drugs.
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Police have reported killing 756 people they have branded drug suspects, although they have insisted they are only acting in self-defense.
The US State Department last week said it was "deeply concerned" about reports of extrajudicial killings.
The UN's special rapporteur on summary executions, Agnes Callamard, also said Duterte's promise of immunity and bounties to security forces who killed drug suspects violated international law.
Duterte responded by threatening to quit the United Nations, saying: "If you are that disrespectful, son of a whore, then I will just leave you."
He later said his threat to withdraw from the UN was a joke, but continued to repeatedly criticize the international body.
And after garnering more bad headlines overseas for calling the US ambassador "gay" and a "son of a whore," Duterte refused to apologize.
The Philippines, a former US colony, was regarded as one of the United States' most loyal allies in Asia until Duterte took office.
The two nations are bound by a mutual defense pact.
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