Japan called the actions of Chinese ships "unacceptable," the Kyodo news agency cited a senior Foreign Ministry official as saying.
Four Chinese coast guard ships on Saturday approached the Senkaku Islands, known as Diaoyu in China, according to the agency.
The Chinese ships reportedly pointed their bows at two Japanese fishing boats, prompting the Japanese coast guard to send its vessels to head them off.
A third ship, apparently armed with a cannon, cruised just outside what Japan sees as its territorial waters. The alleged incursion is the first one since a law took effect in China that allows its ships to open fire on foreign vessels.