By Gregory Poling

The Philippine National Police’s Special Action Force launched a raid on January 25 in Mamasapano on the southern island of Mindanao that killed wanted terrorist Zulkifli bin Hir, known as Marwan, but at the cost of 44 police commandos’ lives. The operation has caused a firestorm in the Philippines, threatening the peace deal the government reached with Moro rebels in January 2014. It has also shaken faith in the Benigno Aquino administration, with opposition lawmakers calling for the president’s impeachment. But the fallout could end up as more than just a domestic crisis and bears watching by U.S. policymakers.

After the raid, Philippine commentators began speculating about U.S. involvement. The Philippine National Police on March 13 released its report about the Mamasapano operation, followed four days later by the findings of a Senate panel of inquiry. Both reports confirmed that U.S. troops did not engage in combat but were involved in training, intelligence gathering, advising, and monitoring the operation. The troops also provided equipment and, according to the police report, medical assistance. The police inquiry found that U.S. support helped commandos “elude large enemy formations, thereby avoiding further casualties.”

But the narrative in the Philippines has not focused on the benefits of U.S. support in the operation. Instead, lawmakers and the public have expressed concern about the unusual level of access for U.S. personnel during an operation about which even the interior secretary and the acting chief of police knew nothing. They have also questioned whether U.S. pressure to capture or kill Marwan pushed the Aquino administration into the operation. Mamasapano has poured fuel on the fire for those distrustful of U.S. intentions and opposed to an increased American military presence in the country—something that was already stoked by the trial scheduled to start next week of U.S. Marine Scott Pemberton for the murder of transgendered Filipina Jennifer Laude.

Both Manila and Washington have trumpeted the Enhanced Defense Cooperation Agreement signed in April 2014 as the cornerstone of a new era in the bilateral security relationship. The agreement would see rotations of U.S. ships, planes, and personnel at Philippine bases, much as U.S. Marines have been doing in Darwin, Australia, in recent years. That rotational presence will allow greater joint training opportunities, boost Philippine capacity, and provide the United States with a forward-deployed presence to respond rapidly to crises in the region. It might also provide an additional deterrent to Chinese aggression in the South China Sea, and is therefore crucial to Manila’s goal of establishing a “minimum credible defense” posture to discourage Chinese adventurism.

The defense security agreement still needs to survive a challenge before the Philippine Supreme Court. Filipino legal experts largely agree that by the strict letter of the law, the court should find the agreement constitutional. But concerns bred by Mamasapano could well feed into any concerns the justices might have about the access granted by the agreement. And with the Philippine judiciary still not an entirely apolitical institution, the weight of public pressure or opposition from influential lawmakers, especially just a year out from a presidential race, cannot be discounted.

Mamasapano could also have long-term implications for whether and to what degree the Philippines can be the security partner the United States hopes it can be. The Aquino administration has made modernizing the navy and air force a top priority, recognizing that the Philippine military must look more to external threats than internal ones. The assumption that the peace process in the southern Philippines will be successful has underpinned that modernization effort. A lasting peace with the Moro Islamic Liberation Front (MILF) would not resolve all of Manila’s internal security concerns—it would still have the communist New People’s Army, the Abu Sayyaf terrorist network, and several Moro splinter groups with which to contend—but it would allow a significant realignment of forces and focus.

Now the fate of the Bangsamoro Basic Law, which would implement the peace deal reached last January ending decades of conflict between the government and the MILF in Mindanao, is uncertain. Lawmakers have attacked various provisions amid anger over the MILF role in the Mamasapano clash, and deliberations on the bill have been suspended until late April.

The successful implementation of the peace deal is crucial to allow the Philippine army to bring more force to bear against the more radical Moro groups that trouble Mindanao and against the Abu Sayyaf group. The military has been prosecuting a campaign with MILF support against the Bangsamoro Islamic Freedom Front since Mamasapano, and another against Abu Sayyaf since December. The campaigns have severely damaged both organizations, but at a terrible cost, with nearly 100,000 civilians displaced. That should provide a sobering warning about the kind of damage renewed war with the MILF could cause.

The United States has a vested interest in seeing Abu Sayyaf destroyed—one that drove the 14-year-long Operation Enduring Freedom–Philippines and that has come into renewed focus since Abu Sayyaf fighters began swearing allegiance to the Islamic State. Washington ended Operation Enduring Freedom last July, in recognition of its success in largely eliminating the threat of international terrorism in the southern Philippines.

On February 24, U.S. soldiers in Zamboanga City on Mindanao held a ceremony to officially deactivate Joint Special Operations Task Force–Philippines, though some U.S. troops are to remain in the Philippines to advise and assist in the fight against Abu Sayyaf. The collapse of the peace process with the MILF would seriously deteriorate the Philippine military’s capacity to press the fight against Abu Sayyaf. That in turn could undermine the successes that have allowed the U.S. drawdown of involvement in the southern Philippines.

The Mamasapano raid and its aftermath have presented the Aquino administration with the greatest challenge it has faced. The potential domestic damage is far reaching. But Washington should not view the matter as one affecting only domestic Philippine political and security concerns. Mamasapano could have very real long-term consequences for U.S. interests.

Mr. Gregory B. Poling is a Fellow with the Sumitro Chair for Southeast Asia Studies at CSIS. Follow him on twitter @GregPoling.