MANILA—A new defense pact between the U.S. and the Philippines faces years in limbo due to legal challenges, frustrating plans to strengthen bilateral ties by dispatching American troops to the Southeast Asian country.

Signed in April to coincide with President Barack Obama's visit to the Philippines, the Enhanced Defense Cooperation Agreement heralded the return of U.S. forces to once-iconic American military facilities such as Clark Air Base and Subic Bay, two decades after they were forced out of the Philippines.

Territorial disputes with China in the South China Sea, and the urgent need to train and re-equip its own neglected military forces, had convinced the Philippine government to welcome U.S. forces back on a rotational basis. This dovetailed perfectly with the Obama administration's policy of rebalancing strategically to the Asia-Pacific, with rotational deployments to Australia and Singapore having already been agreed.

However, American and Philippine government officials in Manila have revealed that talks about the practical details of the U.S. deployment—such as how many troops will come here, and to which locations—have ground to a halt due to a legal challenge before the country's Supreme Court.

A Philippine defense official, who spoke on condition of anonymity, said his government remains confident the case will be thrown out, citing previous examples in which the Supreme Court had sided with the executive branch in matters of defense and foreign policy.