Duterte, who cursed Obama as a "son of a bitch" Monday, said in a statement through his spokesman that he regretted "it came across as a personal attack on the US President."
"We look forward to ironing out differences arising out of national priorities and perceptions," the statement released on Tuesday read.
White House officials previously said
Obama would confront Duterte about his country's handling of drug dealers, including extrajudicial killings
, which are government executions without the benefit of judicial proceedings.
"Who does he think he is? I am no American puppet. I am the president of a sovereign country and I am not answerable to anyone except the Filipino people," Duterte scoffed in a speech Monday. "Son of a bitch, I will swear at you."
A statement from Duterte's office Tuesday claimed the "son of the bitch" insult was aimed at the journalist whose question prompted the fiery response, and not at Obama.
Obama has worked hard to develop the Philippines' partnership with the US and as a regional counterbalance to China. He's visited the country twice in his second term, and announced on a stop there in November the return of a US military presence at a critical naval base on the South China Sea.
But Duterte's derogatory comments and a spike in extrajudicial killings of suspected drug dealers put the relationship in stormier waters.
Obama and Duterte had been set to meet in Laos this week, where Obama is attending a meeting of Southeast Asian leaders. The statement from Duterte's spokesman said the "meeting has been mutually agreed upon to be moved to a later date."
Obama instead met Tuesday with President Park Geun-hye of South Korea.
In his speech Monday, Duterte also blamed the United States for causing the unrest on the southern Philippines island of Mindanao.
"As a matter of fact, we inherited this problem from the United States," he said. "Why? Because they invaded this country and made us their subjugated people. Everybody has a terrible record of extrajudicial killing. Why make an issue about fighting crime?"
Duterte was referring to the US's history as a colonial power in the Philippines, and specifically to one infamous massacre in the southern Philippines -- the 1906 Battle of Bud Dajo -- in which hundreds of Filipinos, including women and children, were killed.
"How many died? Six hundred," Duterte said Monday. "If (Obama) can answer that question and give the apology, I will answer him."
Obama indicated Monday he was wary of meeting with Duterte, suggesting the bombast could prevent making substantial progress between the two nations.
"I always want to make sure if I'm having a meeting that it's productive and we're getting something done," Obama said during a news conference.
"If and when we have a meeting, this is something that is going to be brought up," Obama said, referring to the Philippines' controversial record of combating drug crime since Duterte took office earlier this year.
Later, on Monday afternoon, the White House announced the meeting was canceled.
The Philippines war on drugs
Since Duterte was elected, more than 1,900 people have died,
including at least 700 in police operations that were part of the President's hard-line 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 [been] put behind bars -- or below the ground, if they so wish," Duterte said during his State of the Nation speech on July 25.
Despite the bullish tone, a government spokesman insisted the Duterte administration is against any form of extrajudicial killings.
"We do not condone these acts," Presidential Communications Office Secretary Martin Andanar said.
"(The) government is here to save our people from the drug menace and punish the offenders, including the big-time ones. The PNP (Philippines National Police) continues to investigate situations involving vigilante killings and operational aspects where deaths are reported."
Human Rights Watch has called for
the International Narcotics Control Board and United Nations Office on Drugs and Crime to condemn the "alarming surge in killings of suspected drug users or dealers" in the country.