Japanese Vice Foreign Minister Shinsuke Sugiyama lodged a protest with Ambassador to Japan Cheng Yonghua over the submarine's entry into the contiguous zone, the sources said.
Japan's defense ministry claimed China sent two submarines near Japan-claimed territory, including the Miyako Island in Okinawa and Taisho Island in the Senkakus.
Lu also said that China noticed two Japanese ships approaching the disputed area.
The incident was the first to involve a submarine in the contiguous zone around the Senkakus. The submarine left the zone on Thursday morning, but again sailed into the zone northeast of Taisho Island in the Japanese-administered Senkaku chain later.
Japan and China have always been at loggerheads over the tiny, uninhabited islands in the 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.
Defense Minister Itsunori Onodera said the submarine surfaced Thursday flying a Chinese flag on its mast.
It's not official, but sources say the secretive Zuma satellite was lost
The rocket's second stage propels the satellite into orbit. "This is a classified mission", a spokesperson told NBC News . This is not the first time a payload was lost on a SpaceX mission. "We can not comment on a classified mission", he said.
Meanwhile, the Chinese frigate was spotted in the contiguous zone near the isle on Thursday morning.
Chief Cabinet Secretary Yoshihide Suga told reporters Japan calls on China to "not engage in actions that impede the improvement of bilateral 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.
Ministry officials say the submarine apparently belongs to the Chinese Navy, as a Chinese frigate was spotted nearby. "China's decision to guard the sovereignty of the [Diaoyu] territory is unshaken".
The warship and the submarine had left the waters by the afternoon, the defence ministry said in a statement.
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. A Chinese frigate was last seen in the contiguous zone in June 2016.
"We are monitoring the vessels and sending a message to them that they entered the contiguous waters near Japanese territory", said Yamaguchi.