Obama will fly to Laos from Hangzhou, China, for his 10th and last G20 summit that will run Sept. 4-5.
Obama and Duterte will get together on the sidelines of the East Asia Summit, starting on Sept. 6, the White House announced Monday.
Duterte took power in June, and since then he has instituted a war on drugs. More than 1,900 people have died, including at least 700 as part of police operations.
Duterte, who is known as the "The punisher," won the presidency on a populist, anti-crime platform promising to kill drug dealers. During his campaign he touted his experience arresting petty criminals as the mayor of Davao City, the Philippines' third largest city.
"We absolutely expect [Obama] will raise concerns about some of the recent statements from the president of the Philippines," White House Deputy National Security Adviser Ben Rhodes told media when asked whether Duterte's controversial remarks about vigilante killings, journalists and a woman senator would be discussed. "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. We take the opportunity of those meetings to raise those issues directly."
Obama and Duterte will also discuss the ongoing maritime disputes in the South China Sea. The East Asia Summit comes two months after the Philippines won a major international court battle against China over the disputed sea.
"I think at the same time, of course, we have a very sensitive security environment in the region right now," Rhodes said. "And in the aftermath of the arbitration ruling, it's essential that, just as we will be talking to China about matters related to the South China Sea, that we're also talking to Asian countries and treaty allies like the Philippines, as well."
Rhodes said the meeting will be a chance to discuss both issues.
"So I think that discussion will encompass both concerns about statements that have been made by the president of the Philippines and our commitment to supporting human rights and all efforts that are undertaken bilaterally, and also, again, discussing the regional picture, particularly I think with a focus on the maritime issues," Rhodes said.
On Monday, Duterte launched another scathing attack at Sen. Leila de Lima, saying she should hang herself in shame after being implicated in the drug trade and engaging in immoral behavior. She has been critical of the killings.
Last week, the president said De Lima's political career was "finished" after he released a "matrix" that traced her supposed links to prominent government and police personalities who run or protect a drug network inside the state penitentiary.
And before taking office, he took aim at journalists. "Just because you're a journalist you are not exempted from assassination, if you're a son of a [expletive]," Duterte said. "Freedom of expression cannot help you if you have done something wrong," he added.
Obama's trip to Laos will be the first visit by a sitting U.S. president to the country. He will meet with the president and prime minister.
Obama departs Wednesday from Washington with a stop planned in Nevada to speak at the annual Lake Tahoe Summit with Sen. Harry Reid. Then that evening he will will address leaders from the Pacific Island Conference of Leaders and the IUCN World Conservation Congress to discuss climate change.
On Thursday, he will will travel to Midway Atoll in the North Pacific, where he is scheduled speak about the latest marine national monument.
On Friday, he will depart for China for talks with Xi. The president's meeting with Xi will cover an array of differences between the U.S. and China, including tensions in the South China Sea, the economy, human rights and cybersecurity, Rhodes said.
The United States and China are expected to discuss North Korea's nuclear provocations and the U.S. plan to deploy the Terminal High Altitude Area Defense missile defense system in South Korea.
During the G20 Summit, Obama will meet with Turkish President Recep Tayyip Erdogan for the first time since a military coup was attempted last month.