"You have the EDCA, well forget it. If I stay here long enough," Duterte said. "I do not want to see any military man of any other nation except the Filipino. That's the only thing I want."
In the Philippines, a president is allowed only one six-year term in office, and Duterte did not specify what he meant by staying long enough.
On Monday, US Assistant Secretary of State for East Asia and the Pacific, Daniel Russel, visited Manila in a bid to calm troubled waters and get clarity about Duterte's intentions.
Russel told reporters he loved the Philippines and that the United States remained a trusted partner of the country. But he also made headlines by saying that Duterte's controversial comments had provoked uncertainty and consternation around the world.
Those remarks seemed to get under Duterte's notoriously thin skin.
Duterte lost his cool as he answered questions, holding up the front page of a Philippine newspaper carrying the headline: "Duterte sparking international distress - US".
"You know, I did not start this fight," he said.
Duterte went on to complain about issues ranging from the American bombing of Manila at the end of World War II to embassy officials once questioning his intentions when he applied for a visa to visit his girlfriend, Reuters reported.
China has been extremely unhappy about the heightened US military presence in the Philippines and is likely to welcome Duterte's unease with American troops.
But it is another headache for Obama and setback for his goal of a strategic rebalance to Asia.
If US troops were eventually forced out of the Philippines, it is far from clear where else they could deploy to effectively monitor the South China Sea, experts said, with Singapore and Malaysia quite far south and Vietnam very unlikely to welcome them.
Obama's pivot to Asia is also reeling from the growing problems faced by the Trans-Pacific Partnership.
The TPP, an ambitious trade deal agreed by 12 Asia Pacific nations, was the economic cornerstone of the rebalance, but with both major US presidential candidates opposed to it and Congress extremely wary, ratification looks unlikely, and the whole deal could unravel.