Delfin Lorenzana said US ships and aircraft could use bases in Guam, Okinawa or fly from aircraft carriers to patrol the disputed waters.
Under President Rodrigo Duterte's predecessor, Benigno Aquino III, some US aircraft and ships stopped in the Philippines on the way to patrolling the disputed waters to challenge China's territorial claims.
Duterte, who took office in June, has taken steps to mend ties with China and became hostile toward the Obama administration after it raised concerns over Duterte's deadly crackdown on illegal drugs.
"We'll avoid that for the meantime," Lorenzana said. "Anyway, the US can fly over there coming from other bases." US officials did not comment immediately. The commander of US forces in the Pacific, Adm Harry Harris, said last month that despite Duterte's rhetoric, military cooperation with Manila has not changed.
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Duterte has publicly threatened to scale back the Philippines' military engagements with the US, including scuttling a plan to carry out joint patrols with the US Navy in the disputed waters, which he said China opposes.
Duterte's actions have become a hindrance to US efforts to reassert its presence in Asia, although the US military has vowed to continue patrolling one of the world's busiest commercial waterways.
After Duterte met Chinese President Xi Jinping in Beijing in October, China allowed Filipinos to fish at disputed Scarborough Shoal. China took control of the rich fishing area in 2012 after a tense standoff with Philippine government ships.