China's defense ministry said that a Chinese missile frigate had responded to two Japanese ships entering its claimed waters but that the ships had now left.
Japan's vice foreign minister Shinsuke Sugiyama summoned Chinese ambassador Cheng Yonghua to voice Tokyo's concerns over Beijing's military deployment in the disputed waters.
Japan lodged a formal protest with China on Thursday after detecting a Chinese frigate and an unidentified foreign submarine in waters close to the disputed Senkaku Islands in the East China Sea.
A foreign submarine was also detected in the area on Wednesday, in the so-called contiguous zone near Miyako Island, southeast of the Senkakus, the ministry said, without identifying the nation involved.
The Senkakus - an uninhabited chain surrounded by resource-rich waters between Okinawa and Taiwan - are claimed by Japan, Taiwan and China, which refers to them as Diaoyu.
"Both Japan's Maritime Self-Defense Force and the Chinese navy typically steer clear of the contiguous zone around the Senkakus so as not to provoke one another", former MSDF Vice Adm. Toshiyuki Ito said.
The 4,000-ton Jiangkai-II class frigate was spotted at 11 a.m. sailing near the contested waters, known as the Senkaku in Japan and Diaoyu in China, according to the South China Morning Post.
Beijing said it firmly opposed and was strongly dissatisfied with Japan's actions, which had "mixed up right and wrong", the statement said. It left Thursday afternoon.
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Japanese Chief Cabinet Secretary Yoshihide Suga urged China in his daily press conference not to "take action hindering improvement in Sino-Japanese relations".
Japanese Prime Minister Shinzo Abe responded to the incidents Thursday by giving instructions to prepare for all possible contingencies and to coordinate closely with the US, according to a statement released by his Cabinet.
"The measures by the Japanese side will not change the established fact that the Diaoyu Islands belong to China, nor will it change China's resolution to safeguard its territory in the Diaoyu Islands", Chinese foreign ministry spokesman Lu Kang said during a regular press briefing on Thursday.
The Chinese side explained the move by saying that its navy was in the area to monitor and follow two vessels belonging to Japan.
Maritime confrontations and jet interceptions between China and Japan have become commonplace in recent years, especially around the Senkakus.
The Japan Coast Guard said Chinese ships entered Japanese waters 114 times previous year.
Though the Japanese Defense Ministry has not said the submarine was Chinese, the circumstances suggest that it was likely a PLAN vessel.