"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," Chief Cabinet Secretary Hiroyuki Hosoda, the government spokesman, told reporters in Tokyo on Friday.
Japan summoned Cheng Yonghua, a minister at the Chinese embassy, to hear Japan's protest at 5:00pm (0800 GMT), foreign ministry spokesman Hatsuhisa Takashima said.
Japan had earlier refrained from identifying the submarine, which was spotted near gas fields disputed between the Asian powers.
Chinese submarines are familiar
with the oceana area, Japan said
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 north-west, 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.
The submarine spent about two hours in Japanese waters on Wednesday near the southern island of Okinawa before being chased on the high seas by two Japanese destroyers and a surveillance plane.
Japan had been tracking the sub with wireless microphone buoys dropped from the surveillance plane.
"the relevant departments are maintaining close contact to watch
Chinese Foreign Ministry
China has said only that it was aware of the reports of the submarine and was "watching the situation closely".
"Of course the relevant departments are maintaining close contact to watch this incident," Chinese foreign ministry spokeswoman Zhang Qiyue said on Thursday.
Disputes have been mounting between China and Japan, which are both heavily dependent on energy imports.
China feels deep resentment over Japan's brutal 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.