A foreign submarine was also detected in the same area on Wednesday as well as on Thursday, according to Japan's Defense Ministry.
Japan protested to China on Friday after a foreign submarine in waters near disputed islands in the East China Sea was confirmed to be Chinese, Reuters reports.
The officials say the submarine again entered Japan's contiguous zone on Thursday morning off Taisho Island of the Senkaku Islands. China has probed Japan's claimed waters and air space in the East China Sea with a range of assets so far, including aircraft, drones, and surface ships.
Located around 150 km northeast of Taiwan, the uninhabited Senkaku Islands have an area of about 7 sq km and are said to possibly be rich in marine and energy resources.
In 2004, the government ordered an SDF maritime security operation after a Chinese nuclear submarine intruded into Japanese waters around the Saki-shima island chain, southern Japan.
"Senkaku is Japan's territory and territorial waters internationally and historically and Japan's claim about the contiguous zone is absolutely correct", Defense Minister Itsunori Onodera told reporters Friday morning.
Lu also said Japanese actions in the East China Sea "cannot change the objective fact the Diaoyutai belong to China".
Along with the submarine, a Chinese frigate was identified Thursday as having entered the zone, prompting Japan to protest the action. It left Thursday afternoon.
Japan was monitoring the submarine, but would refrain from releasing details, including its identity, Japan's Chief Cabinet Secretary Yoshihide Suga told a regular briefing.
In a news conference on Thursday, Lu Kang, China's foreign ministry spokesperson, declared that the islands were a part of Beijing's territory and warned Japan to stop complicating the issue, reported NHK World.
Onodera made the statement during a visit to Hawaii Thursday. "China's decision to guard the sovereignty of the Diaoyutai territory is unshaken".
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.
The warship and the submarine had left the waters by the afternoon, the defence ministry said in a statement.