China said it was acting within the confines of the marine law and also adhering to the principles of free navigation.
A Chinese People's Liberation Army-Navy Type 815 Dongdiao-class spy ship entered Japanese territorial waters on Wednesday, according to Japan's defense ministry.
Though the ship didn't enter territorial waters around the islands, known as the Senkaku in Japanese and the Diaoyu in Chinese, the dispute makes the situation there much more charged.
"The government will continue to take all possible measures for warning and surveillance activity for our territorial waters and airspace", Seko said.
Reports added that last week, a separate Chinese naval frigate had passed near a set of uninhabited islands claimed by both countries, leading Japan to pledge to protect its maritime territory. The two allies have been leaders in building worldwide cooperation against Chinese actions to militarize artificial islands in the South China Sea.
A high-ranking official of the Japanese Defense Ministry expressed exasperation, saying, "We have yet to find effective means to make China abide by worldwide rules".
Beijing has been angered by the naval exercises conducted, particularly by USA military patrols that have been seen close to Chinese islands.
Although incursions by Chinese coast guard ships in waters near Senkaku are common, this was the first time a navy ship did so.
"We are getting used to operating in close proximity of Chinese vessels", the official said.
In a related development, the U.S. Navy had announced on June 14 that additional warships from the Navy's third fleet would be moved to work in East and South China seas to work alongside the Seventh fleet based in Japan.
The response from Japan, this time, was more muted, however, with the government conveying its "concerns about the Chinese military's activities in general", Seko said.
The government also hopes to arrange a Japan-China bilateral meeting during this September's Group of 20 summit in Hangzhou, China, to urge Chinese President Xi Jinping to practice self-restraint.