China claims most of the waters, through which $5 trillion in ship-borne trade passes every year. The Philippines, Vietnam, Malaysia, Taiwan and Brunei have overlapping claims, as well as close military ties with the United States.
The Philippines has brought a case at an international tribunal in The Hague contesting China's claims, a case rejected by China which wants to try solve the issue bilaterally.
Duterte has said he will not go to war against China and may hold bilateral talks.
"We must await the decision from (the tribunal) before we start talking to China because otherwise, the judges are going to think twice about what it is that we're doing," former foreign minister Albert del Rosario, who filed the complaint in The Hague in 2013, told reporters.
Ernest Bower, head of the Southeast Asia programme at the U.S. Center for Strategic and International Studies, also cautioned the government against bilateral talks without condition.
"If the Philippines finds a way forward with China that includes China's commitment to forego the nine-dash line claim and commit to a legally binding code of conduct in the South China Sea (Vietnam's East Sea), then go ahead," he told soldiers and diplomats at the main army base in Manila.
But, if there were no such conditions, he said: "I think the Philippines would lose the respect of its partners in ASEAN and certainly the U.S. will be extremely disappointed."
Manila is contesting Beijing's claim to an area shown on its maps as a nine-dash line stretching deep into the maritime heart of Southeast Asia, covering hundreds disputed islands and reefs. ASEAN is the Association of Southeast Asian Nations.
China told the United States on Tuesday that it should play a constructive role in safeguarding peace in the South China Sea (Vietnam's East Sea), as U.S. Secretary of State John Kerry called for talks and a peaceful resolution.