Japan lodged a protest with its neighbor after the submarine and the Chinese vessel approached what Tokyo considers as its territorial waters around the Japanese-administered Senkaku Islands, Japan's Defense Ministry said.
A foreign submarine was also detected in the contiguous waters near Japanese territory on Wednesday and Thursday, said the country's Defence Ministry, which believes that the submarine is also from China, as reported by local news agency Kyodo.
A Chinese frigate was also observed Thursday entering the zone, prompting Japan to protest that action. The first was in June 2016.
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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.
The friction comes despite all the recent positive developments between Asia's two biggest economies, with top political leaders from both sides agreeing to intensify efforts to improve relations.
The officials say a Maritime Self-Defense Force vessel on Wednesday afternoon spotted a submarine sailing underwater off Miyako Island in the southern prefecture. The Japanese government maintains that the islands are an inherent part of Japan's territory. The sub exited the contiguous zone and headed toward the Senkakus on Thursday morning.
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Vice Foreign Minister Shinsuke Sugiyama summoned Chinese Ambassador Cheng Yonghua to lodge a protest on Thursday. "This unilaterally heightens tensions", Onodera told reporters.
In late December, Toshihiro Nikai, secretary general of Japan's ruling Liberal Democratic Party, held talks with Chinese President Xi Jinping, inviting him to visit Tokyo this year.
The mechanism has been subject to a decade of negotiations. Officials from both sides met in Shanghai for two days and made a decision to implement the hotline. It does not include the contiguous zone, where a coastal state is afforded some law enforcement rights under worldwide law. The sailings into the contiguous zone do not present a problem under global law.
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Chinese officials defended the move Thursday, saying that the Senkakus are China's territory and that the incident was instigated by two Japanese navy vessels. The development prompted sharp criticism from China and triggered frequent intrusions by China Coast Guard vessels into Japanese waters around the islets.