In a statement, the president clarified that he did not mean his comments as a personal attack on Obama, GMA News reported.
"While the immediate cause was my strong comments to certain press questions that elicited concern and distress we also regret it came across as a personal attack on the US president," he said.
Obama's camp recently said they have canceled the meeting with Duterte following his remarks that called the US president a "son of a whore."
However, the meeting was just rescheduled to a later date, according to Duterte.
"We look forward to ironing out of difference arising out of national priorities and perceptions, and working in mutually responsible ways to both countries," he said.
Duterte made the controversial remarks on Monday, prior to his flight to Laos where he is scheduled to attend a gathering of world leaders at the ASEAN summit.
During a press briefing, he responded to a reporter's question by asking why he had to answer to Obama on the issue of extrajudicial killings in the country, adding that he only considers the Filipino as his master.