China has denied any wrongdoing, saying it was conducting a "normal exercise." The incursion comes amid joint military exercises between Japan, the US and India.
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A Chinese "information gathering" vessel on Wednesday entered Japanese territorial waters, prompting Tokyo to voice "concerns about the Chinese military's activities in general," said officials.
"The Chinese military vessel moved in after an Indian ship sailed into Japan's territorial waters as it participated in a Japan-US-India joint exercise," said Japanese Defense Minister Gen Nakatani.
China's defense ministry said its vessel acted in accordance with international law and the principle of freedom of navigation.
"The government will continue to take thorough measures to patrol the air space and waters surrounding our nation," said Deputy Chief Cabinet Secretary Hiroshige Seko in a statement.
Wednesday's incursion marks the first time a Chinese naval vessel has entered Japanese waters since 2004, when a Chinese nuclear submarine was detected near the Ishigaki Island.
Beijing's island-building in the South China Sea
Satellite images show the extent and speed of China's land reclamation activities in disputed waters of the South China Sea. The new land masses are believed to be primarily military installations.
Image: CSIS Asia Maritime Transparency Initiative/DigitalGlobe
Runway
China is expanding the construction of its facilities on Fiery Cross Reef. Provided by the Asia Maritime Transparency Initiative (AMTI), this June 28, 2015 photo reveals Beijing has nearly completed a 3,000 meter (9,800-foot) airstrip, long enough to accommodate most Chinese military aircraft. Two helipads, up to 10 satellite communications antennas, and one possible radar tower are also visible.
Image: CSIS Asia Maritime Transparency Initiative/DigitalGlobe
Expansion
Reclamation on Fiery Cross Reef, which lies on the west side of the Spratly Islands, began in August of 2014 and its principal landmass was finished by November. Dredgers have created a land mass that spans the entire existing reef and is approximately 3,000 meters long and 200-300 meters wide.
Image: Reuters//U.S. Navy
Facilities
This picture taken last November shows construction work being carried out on Fiery Cross Reef. The reef reportedly already houses a helicopter landing pad, a 300-meter-long wharf, a harbor large enough to dock military tankers, barracks and artillery emplacements.
Image: CSIS, IHS Jane's
South Johnson Reef
This reef was one of the first facilities to finish principal land reclamation. This recent picture shows that a radar tower is nearing completion at the north end of the land mass. According to AMTI, a new large multi-level military facility has been built in the center of the island. Up to six surveillance towers are being constructed alongside four possible weapons towers.
Image: Asia Maritime Transparency Iniative
A naval base?
Beginning in early 2015, Mischief Reef - also located in the Spratlys - has undergone extensive reclamation activity. Experts say that the recent widening of the southern entrance to the reef, coupled with sightings of Chinese navy vessels, may suggest a future role for the reclaimed reef as a naval base. Taken on March 17, this image shows a chain of small land formations at the reef.
Image: CSIS Asia Maritime Transparency Initiative/DigitalGlobe
From reef to island
Significant construction on Gaven Reef began in 2014, with a total of 114,000 square meters of land already created. Satellite pictures show just how fast construction has progressed on the reef. A new artificial island was created between March (left) and August (right) 2014.
According to AMTI, China has had a troop garrison on Gaven Reef since 2003, which has included a large supply platform where ships can dock. Experts say a new main square building in the reef appears to be an anti-aircraft tower.
Image: AMTI
A standardized process
As seen in this image, the basic process of expanding these features involves dredging sand from the seafloor and dumping it onto the reefs. The structure is raised above the high water line, hiding the status of the bank or reef beneath. The sand is then smoothed out and workers surround the island with a concrete barrier to protect against erosion and storm surge, and begin construction.
Image: CSIS
'Historic rights'
China claims most of the potentially energy-rich waterway, through which $5 trillion in ship-borne trade passes every year. The US Pacific Fleet commander recently said China was "creating a great wall of sand" in the South China Sea, causing serious concerns about its territorial intentions. Beijing argues it is asserting its so-called "historic rights" to maritime resources in the area.
Image: DW
Territorial disputes
The Philippines, Vietnam, Malaysia, Brunei and Taiwan also have overlapping claims, which have led to territorial disputes in the area. Last summer, China's deployment of a massive oil rig in waters also claimed by Hanoi escalated tensions in the region, sparking a standoff at sea and violent anti-Chinese demonstrations in Vietnam.
Image: picture alliance/AP Photo
US concerns
Washington is concerned China's efforts carry a military dimension that could undermine the US' naval and economic power in the Pacific, and has weighed sending warships and surveillance aircraft within 12 nautical miles of the new artificial islands. Washington has repeatedly called on Beijing and others to end reclamation projects in the disputed waters, but Beijing rejects those demands.
Image: Getty Images/AFP/M. Abbugao
Ecological impact
The Philippines filed a formal plea at the UN last year, challenging Beijing's territorial claims. Manila said China's reclamation activities are causing "irreversible and widespread damage to the biodiversity and ecological balance of the South China Sea." It also claimed that the destruction of coral reef systems is estimated to cause economic losses valued at $100 million annually.
Image: CC2.0/TheAnimalDay
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Disputed areas
In the South China Sea, tensions have risen between China and its neighbors Taiwan, Malaysia, Brunei and the Philippines, which claim areas Beijing says are an integral part of its territory.
However, the Association of Southeast Asian Nations (ASEAN) on Tuesday retracted a strongly worded statement warning of rising tensions in the South China Sea, although China was not directly mentioned.
"We expressed our serious concerns over recent and ongoing developments, which have eroded trust and confidence, increased tensions and which may have the potential to undermine peace, security and stability in the South China Sea," said a statement from the regional group.
Earlier this year, US President Barack Obama said Washington is committed to supporting the ASEAN community in light of the latest developments in the contested sea.
"We discussed the need for tangible steps in the South China Sea to lower tensions including a halt to further reclamation, new construction and militarization of disputed areas," Obama said, referring to China building artificial islands holding military assets.