The row over the waters - a major global shipping route thought to be rich in oil and gas reserves - has for years marred China's relationship with the Philippines and other neighboring countries with rival territorial claims.
It was on Wednesday, the first day of Duterte's China visit, when the unidentified owner of the Chinese fishing boat that sank and abandoned a Filipino-owned vessel finally apologized for the incident.
The 2016 Hague arbitration ruling mostly invalidated China's claim to virtually the entire South China Sea and found that it violated the U.N. Convention on the Law of the Sea.
Philippine President Rodrigo Duterte has always downplayed the event referring to it as a "little maritime incident" perhaps not wanting to cause any distractions from his scheduled talks with Chinese leader Xi Jinping that are now underway. After meeting Xi on Thursday and Premier Li Keqiang on Friday, Duterte will fly to Guangzhou on Saturday and watch a basketball match with Vice-President Wang Qishan. The gist of the message: China must accept the worldwide norm that rule of law is a value for all, not an arbitrary tool of the powerful.
Tensions have been building up since China began transforming a string of disputed reefs into missile-protected island bases. The case, initiated by Duterte's predecessor, resulted in a near-complete victory for Manila - most notably the repudiation of China's claims to "historic rights" over features in the Philippines' exclusive economic zone.
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A joint report by the Philippine Coast Guard (PCG) and Maritime Industry Authority (Marina) found that the June 9 allision of Gem-Ver1 and the Chinese boat at Recto Bank was a "very serious marine casualty" due to the total loss of the Filipino fishing vessel.
Mr Santa Romana added that there were also concerns that an outright ban would have a negative effect on the Philippine economy.
On the two countries' possible joint oil and gas exploration, Xi "said that the steering committee created for that objective should prepare a substantive program on the matter", according to the spokesman. "At present, the worldwide and regional situations are undergoing profound and complex changes".
India believes that any difference must be resolved peacefully by respecting the legal and diplomatic processes, and without resorting to threat or use of force, he said.
Duterte will be in China until September 1.