Washington called the fishing rules "provocative and potentially dangerous", prompting a rebuttal from China's foreign ministry on Friday.
Ties between China and Japan, the world's second- and third-largest economies, have been strained due to a long-running row over ownership of the group of tiny, uninhabited islands called the Senkaku in Japan and Diaoyu in China.
Tensions soared in recent months after Beijing announced the air defense identification zone covering a large swathe of the East China Sea, including the disputed isles, and Japanese Prime Minister Shinzo Abe visited a controversial Tokyo shrine seen by critics as a symbol of Japan's wartime aggression.
China and South Korea, where bitter memories of Japan's past militarism run deep, have repeatedly expressed anger in the past over Japanese politicians' visits to Yasukuni Shrine, where Japanese leaders convicted as war criminals by an Allied tribunal are honoured along with those who died in battle.
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Stoking tensions further, three Chinese government ships on Sunday morning briefly entered what Japan sees as its territorial waters near the disputed islands, controlled by Japan but also claimed by China, the latest in such occasional entries by Chinese ships.
"We can never overlook such repeated entries. In addition to diplomatic efforts, we will cooperate with Coast Guard and securely defend our territory and territorial waters around the Senkaku," Onodera said.
Patrol ships from China and Japan have been shadowing each other near the islets on and off for months, raising fears that a confrontation could develop into a clash.