Japan concluded last week that a nuclear-powered submarine that intruded into its waters off the Okinawa islands, 1600km southwest of Tokyo on Wednesday belonged to the Chinese navy and demanded an apology from Beijing, which later said it was looking into the matter.
On Friday, Japan summoned a Chinese diplomat after determining that the vessel that entered its waters near a disputed gas field and set off a high-seas chase came from its giant neighbour.
"We have judged the submarine to belong to the Chinese navy and it's likely the submarine was a nuclear submarine and through diplomatic channels we are going to protest to China," government spokesman Chief Cabinet Secretary Hiroyuki Hosoda said in Tokyo.
Japan had earlier refrained from identifying the submarine, which was spotted near gas fields disputed between the Asian powers.
But Japan's defence chief said the country had determined the submarine was Chinese during the two-day search that ended on Friday.
"As the submarine navigated north by northwest, we determined it belonged to China as the country possesses nuclear-powered submarines in the area and has thorough knowledge of geographical features of the ocean area," Defence Agency Director General Yoshinori Ono said.
A Japanese surveillance plane
chased the submarine
The submarine spent about two hours in Japanese waters on Wednesday near the southern island of Okinawa before being chased by two Japanese destroyers and a surveillance plane.
The submarine was tracked with wireless microphone buoys dropped from the surveillance plane.
China said it was aware of the reports of the submarine and was "watching the situation closely".
China feels deep resentment over Japan's occupation of the country from 1931 to 1945.
The feeling has been regularly reinforced by Prime Minister Junichiro Koizumi's visits to a Tokyo shrine that honours Japanese war dead, including convicted war criminals.