Ties between Asia's two largest economies have long been overshadowed by arguments over their painful wartime history and a territorial spat in the East China Sea, among other issues.
China has repeatedly denounced interference by the United States and its ally Japan in the South China Sea.
Japan will also help build the capacity of coastal states in the busy waterway, its defense minister said last week during a visit to Washington.
Chinese Foreign Ministry spokesman Lu Kang said countries in the region had reached a consensus that the South China Sea issue should be resolved through talks between the parties directly involved, and that China and Southeast Asian countries should jointly maintain peace and stability there.
"Let's have a look at the results of Japan's throwing things into disorder over this same time period ... trying to confuse the South China Sea situation under the presence of (acting for) the international community," Lu told a daily news briefing, when asked about Japan's announcement.
Japan's actions have simply pushed other countries away from it, and it has failed to compel other nations to see its point of view, he added, Reuters said.
"China is resolute in its determination to protect its sovereignty and maritime interests," Lu said.