The incursions happened Wednesday and Thursday in Japan's contiguous zone around Okinawa and the Senkaku Islands by a Chinese frigate and submarine presumed to be from China, Japanese officials said.
Thursday marked the first known time that a submerged foreign submarine entered the contiguous zone, an area just outside Japanese waters around the Japan-controlled, China-claimed islands.
Though the Japanese Defense Ministry has not said the submarine was Chinese, the circumstances suggest that it was likely a PLAN vessel.
Japan's vice minister for foreign affairs Shinsuke Sugiyama summoned Chinese ambassador Cheng Yonghua to voice Tokyo's concerns, as the two Asian giants explore ways to ease bilateral tensions, complicated by North Korea's nuclear and missile drive. On Thursday, Japan issued a warning to China to stand down after a military warship and submarine were seen near the disputed waters in East China Sea.
Beijing said it firmly opposed and was strongly dissatisfied with Japan's actions, which had "mixed up right and wrong", the statement said. It then re-entered the contiguous zone around Taisho Island, which is part of the Senkakus, before leaving that afternoon. It left Thursday afternoon. Therefore, the region of Northeast Asia and the East China Sea doesn't need heightened tensions between China and Japan - or China and Taiwan.
Onodera made the statement during a visit to Hawaii Thursday. A defense ministry spokesman declined to discuss the measures being taken.
Ministry officials say the submarine apparently belongs to the Chinese Navy, as a Chinese frigate was spotted nearby.
In Beijing, foreign ministry spokesman Lu Kang told a regular press briefing "the Chinese naval vessels conducted surveillance over the activities of the Japanese side" and repeated China's claim to the islands.
China routinely rejects Japanese criticism of such patrols, saying its ships have every right to operate in what China calls its territorial waters.
Maritime confrontations and jet interceptions between China and Japan have become commonplace in recent years, especially around the Senkakus.
The ministry is closely monitoring the submarine's move and collecting information.
For example, in 2016, for the first time in years, a PLAN frigate entered the contiguous zone of the Senkaku Islands.