The group of islands in the East China Sea, called the Senkaku in Japan and Diaoyu in China, are historically Japan's territories, Chief Cabinet Secretary Yoshihide Suga told Reuters on Tuesday in an interview.
Japan hopes to respond calmly to the territorial dispute over the islands, Suga added.
Ties between Asia's two largest economies have long been plagued by arguments over their painful wartime history and a territorial spat over the tiny uninhabited isles in the East China Sea as well as regional rivalry and mutual mistrust.
"It is clear the Senkaku islands are historically Japan's territories," said Suga.
Tension mounted earlier this month after more than a dozen Chinese coastguard and other government ships sailed near the group of disputed islets.
Japanese Foreign Minister Fumio Kishida, in a Tokyo meeting with his Chinese counterpart Wang Yi last week, demanded the Chinese side bring the East China Sea situation completely under control and prevent recurrences. Kishida said Wang told him that China hoped to improve ties through dialogue.