The U.S. surveillance missions were focused on monitoring Chinese activity in areas that both China and the Philippines claim as their own, Kyodo News reported Monday.
China has claimed almost all of the South China Sea, including the Scarborough Shoal and the Spratly Islands, which the Philippines also claims.
"[There were] confirmed flights of U.S. P3C Orion aircraft over the South China Sea especially [in the contested Spratly Islands]," said a classified Philippines government document.
Last year, Philippine President Benigno Aquino said his country asked the United States to fly P3C Orion spy planes over the disputed area to monitor the Philippines' territorial and maritime claims in the sea.
"We can only do [the] best [with] what we have," the document said. "The military is aware of its limitations as regards equipment, naval and air assets, facilities and funding to support our efforts" in the South China Sea.