The two countries have long been embroiled in a bitter dispute over their competing claims to the region -- with China claiming nearly the entire sea -- but Duterte has in recent years softened his predecessors' policy of opposing Beijing's claims.
Duterte said yesterday an arrangement to turn two of the rival claimants virtual joint owners of the strategic and supposedly oil and gas-rich sea was preferable to the "massacre" of Filipino troops in a war with China.
Negotiations between the Philippines and China over South China Sea exploration were raised last month by Filipino Foreign Secretary Alan Peter Cayetano.
Presidential spokesman Harry Roque provided more detail today, specifying that talks were underway between the Philippines' energy department and an unnamed Chinese state firm, and that extraction of energy resources was now on the table.
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He did not specify which specific area of the sea was under discussion.
"We might enter into an agreement with a Chinese-owned corporation, not the Chinese state itself," Roque said in an interview aired on ABS-CBN television, adding the company he declined to name was state-owned.
"I know that they're discussing, they're moving forward and it's likely to happen," he added without giving a timetable or the exact terms of the proposed deal.
"This will now actually entail joint exploration and possible exploitation of natural resources."
Aquino won an international arbitration tribunal ruling in 2016 invalidating Beijing's claims, but Duterte set aside the ruling while courting investments and trade from the Philippines' giant neighbour, the world's second-largest economy.
Cayetano said last month that Manila would consult legal experts to make sure any accord would not infringe on Philippine sovereign rights.
"It's not that we have no choice. We can go back and say, 'Fine, no one benefits from the resources now'. But come on, we're trying to look for alternative sources of energy," Roque said today.
He was referring to a 2011 incident when Manila said Chinese patrol boats harassed a seismic survey vessel chartered by a unit of a Philippine mining company at Philippine-claimed Reed Bank in the South China Sea.