At its height, the mission had as many as 600 troops, and it was formally ended in February 2015. However, a small contingent of American advisers, numbering in the dozens, was left behind to provide logistics and support for Philippine forces.
On Monday, Duterte said in a speech that the U.S. military presence on Mindanao was more of a negative than a positive.
"The special forces, they have to go," said Duterte. "They have to go in Mindanao. There are many whites there. They have to go."
He added, "I do not want a rift with America, but they have to go."
"We are aware of President Duterte's statements and refer you to his office on any questions," said Commander Gary Ross, a Pentagon spokesman. "We have not been contacted by authorities regarding this issue."
"We continue to focus on our broad relationship with the Philippines, and will work together in the many areas of mutual interest to improve the livelihoods of the Philippine people and uphold our shared democratic values," said Ross.
"U.S. special forces have been providing support and assistance in the southern Philippines for many years, at the request of several different Filipino administrations," said Ross. He added that over the last two months there have been senior consultations underway "on ways we could increase our assistance to support the new administration's counter-terrorism efforts. We will continue to consult closely with our Filipino partners to appropriately tailor our assistance to whatever approach the new administration adopts."
But Duterte said during his presidential campaign that he would seek to scale back the relationship with the U.S.
One U.S. official said Monday that Duterte's comments appear to be specifically about the small number of American advisers in the Philippines and do not affect the broader agreements announced earlier this year.