When President Benigno Aquino and Secretary of Foreign Affairs Albert Del Rosario of the Philippines met with President Obama and Secretary of State Hillary Clinton in Washington some days ago, they talked about everything under the sun—except the multiple insurgencies that have been festering sores in the Philippines for decades.

From public appearances and press briefings, it seems the Filipino and American leaders ranged over threats to freedom of navigation in the South China Sea, the need to share more intelligence, the desire for better consultation on security issues, the benefits of expanded trade and people-to-people exchanges.

But apparently they did not touch on the internal peril caused by the insurgencies of the Moro National Liberation Front, the Moro Islamic Liberation Front, the Abu Sayyaf and Jemaah Islamiya terrorists linked to al Qaeda, the militant arm of the Communist Party of the Philippines, or private armies like that of the Ampatuan Muslim clan.

Much of these insurgencies is centered on the island of Mindanao in the southern Philippines. There, says Zachary Abuza, a specialist on terror who teaches at the National Defense University in Washington, violent clashes “are part of the culture of Mindanao, where guns and blood feuds are deeply embedded.”

The critical question: Why has the government in Manila, with substantial help from the United States, not been able to quell these insurgencies?

Resolving them has become urgent for the U.S. with the new focus on the vital shipping lanes through the South China Sea to the west of the Philippines. Having an unstable flank along the eastern shores of that sea could make it hard to protect those passages from pirates and terrorists.

Moreover, as Obama officials execute a “pivot” toward the Pacific or seek to “rebalance” the U.S. security posture in this region, they have begun talk of gaining access to Philippine bases and operating more with Filipino forces. That will not be easy if the Philippines are preoccupied with internal crises.

And for the nations of Southeast Asia, the prospect of the southern Philippines becoming a training base and sanctuary from which terrorists could launch operations into the neighborhood would not be a happy one.

The issue is more political than military. David Maxwell, retired colonel of Special Forces and onetime commander of U.S. advisors in Mindanao, says: “The key to understanding insurgency is that it is usually a political or economic problem first and foremost, which has implications for the military.”

The government in Manila, however, has shown itself to be ineffective and riddled with corruption. President Aquino was elected in 2010 on an anti-corruption platform but progress has been slow.

Centuries of Muslim resentment in Mindanao against Christian rulers in Manila has its roots in 350 years of Spanish rule that lasted until the end of the 19th century. The U.S., the colonial ruler until 1946, and the Philippine government since then have continued to be targets of Muslim resentment.

Militarily, the Armed Forces of the Philippines (AFP) have so far been no match for the insurgents. Abuza writes that the AFP has been “poorly trained, ill-disciplined, and mired in corruption.” When U.S. special operations forces moved in to help ten years ago, they found AFP soldiers not well trained in fundamentals.

American soldiers who served there at that time said the Filipinos couldn’t shoot well, did not maintain their weapons, could not find their way through unmarked terrain, failed to patrol aggressively, and tended to rely on informants for information rather than to go see for themselves.

About the time of the Sept.11, 2001 terrorist attacks in New York and Washington, the U.S. formed a task force of special operations troops drawn from all four services and deployed it to the southern Philippines. They were explicitly ordered to train and assist the AFP but not to engage in combat.

Over the years, the special operations troops have had some success in improving the AFP’s fundamentals and in helping to forge tactics to deny insurgents sanctuary, to cut their lines of communication and transport, to block their access to resources, and to separate them from the Philippine people.

Maxwell said in a Congressional hearing recently this has not been easy. “A problem that most U.S. forces have is that they are so focused on mission accomplishment they often lack the patience to let the host nation operate in accordance with its own capabilities as well as customs and traditions.”

“The only people capable of defeating an insurgency are the indigenous government and its indigenous forces,” he says. “We cannot do it for them.”