The Japanese government said the protest has been sent to the Chinese side through the diplomatic channels.
Earlier on Tuesday, three Chinese patrol vessels were seen in the area to the north-west of the Kubadzima Island.
This is the first such incident after Japanese Prime Minister Shinzo Abe and Chinese President Xi Jinping met on the sidelines of the Asia-Pacific Economic Cooperation (APEC) summit in Beijing.Tensions over the group of uninhabited islands increased in September 2012 after Tokyo announced plans to buy them from private owners. After that move, mass anti-Japanese protests hit China.
Since then, Chinese vessels have been repeatedly seen near the disputed Senkaku Islands, also known as the Diaoyu Islands in China.
Japan’s coastal guards have asked to double their budget in 2015 to $447 million to buy new patrol vessels and aircraft and organize round-the-clock patrolling of the area.
Beijing maintains that Japan had annexed the islands by force and they should be given back to China under the terms of Tokyo’s surrender during World War II. Japan has refused to negotiate the issue.