The comments follow a series of anti-American tirades by the firebrand leader, who has repeatedly attacked the US while cosying up to Beijing, upending his nation's foreign policy in comments that have sometimes been quickly retracted.
"I want, maybe in the next two years, my country free of the presence of foreign military troops," Duterte told an economic forum in Tokyo, in a clear reference to US forces.
The US, which once operated sprawling bases in the country, now has a small number of Special Forces on the southern island of Mindanao to aid in counter-terrorism operations.
Duterte has previously said he wants US troops out of Mindanao because their presence stokes tensions on the island where Islamist militants have waged a decades-long separatist insurgency.
Duterte's aides frequently attempt to walk back his controversial comments, and today was no exception.
Foreign Secretary Perfecto Yasay, asked at a subsequent press conference to clarify the remarks, said that Duterte did not mean US troops would be ousted, stressing that "our national interests still continue to converge".
The 71-year-old has also slammed Washington for questioning his violent crime crackdown, which has claimed some 3,700 lives and attracted widespread international criticism.
Duterte has also insulted President Barack Obama, calling him a "son of a whore" and announcing a "separation" from the US during a visit to Beijing last week.
Although he quickly walked back from his comments, saying that "separation" did not mean he would "sever" ties, he reiterated his calls today for an end to all joint war games with the US.
Duterte later began a summit with Prime Minister Shinzo Abe and will also meet with Emperor Akihito tomorrow.
Although his Japanese hosts depend on the US for security, Tokyo has so far not responded to Duterte's diatribes, while Washington has taken a calm approach.
"We're going to take the long view," State Department spokesman John Kirby said yesterday.
"We're not going to react and respond to every bit of rhetoric," he added.
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