The two leaders will talk on the sidelines of the East Asia Summit in Laos, starting on September 6. It will be their first meeting since Duterte took power in June.
"We absolutely expect (President 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 women would be on the agenda.
Rhodes said Obama regularly brought up issues around human rights offenses with treaty allies such as the Philippines.
Since Duterte took office, more than 1,900 people have died, including at least 700 in police operations as part of the president's hardline war on drugs.
"Double your efforts. Triple them, if need be. We will not stop until the last drug lord, the last financier, and the last pusher have surrendered or put behind bars -- or below the ground, if they so wish," Duterte said during his State of the Nation speech on July 25.