Ambassador Philip Goldberg said the security threat in the conflict-plagued region was "very serious", warning the Islamic State group was among a number of foreign militant organisations trying to increase its involvement there.
"We've helped the Philippines as it has reduced the threat over time," Goldberg told ABS-CBN television.
"But we are concerned obviously about any new intrusion of ISIS (Islamic State group) or any other group that wants to take advantage of open space in the south of the Philippines. So we want to continue doing that."
The presence was scaled down after the United States deemed the militants there had "largely devolved into disorganised groups resorting to criminal undertakings", according to a US statement in 2014.
Islamic militant attacks spiked after that, most prominently with the homegrown Abu Sayyaf group abducting dozens of foreigners and locals to extort ransoms.
About 100 American troops remain in the south, Goldberg said today.
But Duterte, who took office on June 30, has said they are adding to tensions with the Islamic communities in the southern region of Mindanao.
Duterte, who describes himself as a socialist and part Muslim, has called for their ejection as part of a general effort to dilute his nation's 70-year alliance with the United States.
Islamic militants have waged a decades-long separatist insurgency in Mindanao that has claimed more than 120,000 lives.
The region is the ancestral homeland of the Muslim minority in the mainly Catholic Philippines.
The major rebel organisations are no longer waging armed struggle, but harder-line splinter groups such as the Abu Sayyaf have remained a threat.
"This is a very serious issue," Goldberg said.
"We are not just dealing with Abu Sayyaf but groups from the region like Jemaah Islamiyah. We see increasing efforts from ISIS to become involved.
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