Last year a United Nations-backed international tribunal rejected Beijing's claims to most of the South China Sea, including disputed areas close to the coasts of its neighbours.
But Duterte, elected last year, has played down that ruling and pushed for rapprochement with China as he seeks billions of dollars in trade and investment from it.
China this week offered to host a meeting in May of a "bilateral consultation mechanism" to tackle issues related to the sea row, the Philippine foreign department said.
China rejects the tribunal's ruling and asserts sovereignty over almost all of the South China Sea, despite partial counter-claims from Brunei, Taiwan, Malaysia, the Philippines and Vietnam.
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It has extensively reclaimed reefs and installed military and other facilities including airstrips on some outcrops.
China has always favoured bilateral talks with each rival claimant instead of negotiations involving all six, as was previously favoured by the Philippines.
Analysts say direct talks with smaller neighbours would allow China to exert its massive economic and political leverage in a region dependent on Chinese trade.
"What is important is we have a peaceful means (to resolve the dispute)," he added.
Duterte, 72, has repeatedly said he does not want to go to war with Beijing over the sea row.
After his election he pivoted his nation's foreign policy away from traditional ally the United States towards China.
Jose said the direct talks would be the "platform" where the Philippines could raise issues like China's construction of artificial islands.
Both nations were still finalising the agenda, dates and level of representation, he added.
"Through this bilateral mechanism, mutual trust and maritime cooperation will be forged and misunderstandings will be avoided," Ernesto Abella said.
Duterte last week heaped praise on China for improving trade relations and for supposedly committing not to build on another disputed shoal that lies even closer to the Philippines than the reclaimed reefs.
"China has a word of honour," Duterte said. "Whatever China says, in good stead, it will really do.