Tokyo on Monday rejected Chinese protests over the raising of a Japanese flag on one of the Diaoyu islands, but called for progress in "mutually beneficial" relations with Beijing.
Chief Cabinet Secretary Osamu Fujimura said Beijing objected after 10 Japanese nationalists' landing on Sunday.
Fujimura said Japanese authorities were handling the case "in accordance with domestic law" as the nationalists broke regulations banning landing on the islands.
"The Japan-China relationship is one of the most important bilateral ties for Japan," he added.
"China's constructive role is necessary for the stability and prosperity of the Asia-Pacific region," he said. "We would like to continue to further progress mutually beneficial relations between Japan and China."
Fujimura also called on the Chinese government to ensure the safety of Japanese nationals in China as anti-Japan protests broke out there targeting Japanese businesses, restaurants and cars.
The Japanese foreign ministry has separately issued a travel advisory, telling Japanese nationals to be on alert while staying in the country.