The remarks during a high-profile visit to Japan follow a series of anti-American tirades by the firebrand leader.
"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, ahead of a summit with Japanese Prime Minister Shinzo Abe.
"I want them out and if I have to revise or abrogate agreements, executive agreements, I will," he added, according to AFP.
The US has a small number of Special Forces on the southern island of Mindanao to aid counter-terrorism operations.
But Duterte has already said he wants US troops out of Mindanao because their presence stokes tensions on the island.
Duterte has repeatedly attacked the US while cozying up to Beijing, upending his nation's foreign policy in comments that have sometimes been quickly retracted.
Philippine Foreign Secretary Perfecto Yasay, asked to clarify the president's remarks, said that Duterte did not mean US troops would be ousted, stressing that "our national interests still continue to converge".
The acid-tongued leader arrived in Tokyo on Tuesday on his first visit to Japan since taking office on June 30, looking to persuade executives his country is "open for business", after seeming to overturn Manila's traditional diplomatic alliances.
The 71-year-old has slammed Washington for questioning his violent crime crackdown, which has claimed some 3,700 lives and attracted widespread international criticism.