The concern has grown more urgent in recent months. ISIS-linked militants there have urged supporters in the region to “join the mujahideen in the Philippines” if they cannot travel to take part in the group's main fight in Syria and Iraq. Since then, cities in Indonesia, Thailand and Malaysia have been attacked.
More recently, the Philippines' newly elected president, Rodrigo Duterte, has called for an end to the U.S. military's counter-terror mission in the Pacific's nation's volatile south. He's also questioned the two countries' broader alliance.
Sen. Joni Ernst, an Iowa Republican, has called for increased attention on the issue, saying the region is a potential breeding ground for terrorist plots if the militant groups who operate there aren’t closely monitored.
"Joint military drills and training with the Philippines is something that I've called on this administration to increase and refocus on to counter ISIS in Southeast Asia, who has started to band together previously splintered radical Islamic extremist groups in the region,” she said last week. “If we don't show American leadership and strong support for our allies that want and need our help against a common enemy, I fear we will see our allies look elsewhere for help.”
The Asia-Pacific region has been a key focus of President Barack Obama's foreign policy. Over the last several years, military rotations and engagements there have increased in large part to reassure America's allies as China has sought to expand its influence.
The terror threat is another matter entirely. In the Philippines, U.S. counter-terror efforts date to 2002 and the rise of Abu Sayyaf, which has sought to establish a separate Muslim state. In 2014 its leaders swore allegiance to ISIS. The U.S. greatly reduced that mission last year, and now only a small group of American forces remains to advise the Filipino military and provide intelligence support.
Joint Chiefs Chairman Gen. Joseph Dunford said he broached the topic during a meeting with foreign defense leaders in early September, given the problems they see in and from the region.
“There are a thousand foreign fighters alone that we estimate have come from Indonesia into Syria and Iraq,” he told lawmakers at the hearing. “There are hundreds that came from the Philippines. Other countries as well are dealing with that issue.”
But Dunford also expressed confidence that military leaders in the region are coordinating with other U.S. agencies to combat the problem. It's unclear whether this new political friction between Washington and Manilla might change that calculus.
Duterte has established a frosty relationship with Obama, warning the American president not to lecture Philippine leaders about human rights and calling him "a son of a whore" for broaching the topic.
He has said there are no plans to dump his country’s defense treaty with the United States. But Duterte contends that joint combat exercises between the two countries benefit only America, and he has since ordered his military leaders to scale back.
The Pentagon has said that any reduction in joint military drills and coordination could reduce both nations’ ability to respond to regional crises.
Rachel Stohl, a senior associate at the Stimson Center, said the United States has sent more than $570 million in security assistance and more than $2 billion in arms sales to the Philippines in the last 15 years, even as outside concerns have mounted over human rights abuses connected to Duterte’s crackdown on the drug trade.
Stohl said those financial ties need to be re-evaluated. “The United States should not let counterterrorism priorities override the potential risk of human rights violations."
But Ernst said U.S. officials can’t afford to overlook the ISIS threat in the region by cutting ties to the country.
“While I remain concerned about alleged human rights violations in the region, it is my hope that our long history of working with the Philippines is not over,” she said. “It's important they know we are a dedicated friend and ally.”
At the Association of Southeast Asian Nations defense meeting in Hawaii on Oct. 1, Carter requested a workshop in early 2017 on counterterrorism and strategy gaps to help tackle the long-term ISIS problems in the region. Ernst called that “a step in the right direction, but we must do more."
Leo Shane III covers Congress, Veterans Affairs and the White House for Military Times. He can be reached at email@example.com.