The anti-submarine drill was conducted on Thursday in the region to "improve strategic techniques", Japan's defence ministry said in a short statement.

Prime Minister Shinzo Abe defended the drill, which he said does not aim to target "a particular nation."

Neither Abe nor a ministry spokesman said whether it was the first such exercise there.

The Asahi Shimbun newspaper said the submarine Kuroshio joined three Japanese warships in waters just southwest of the China-controlled Scarborough Shoal.

China claims most of the resource-rich South China Sea, through which $5 trillion in shipping trade passes annually, despite competing claims from Brunei, Malaysia, the Philippines, Taiwan and Vietnam.

Tensions have been high over the Scarborough Shoal since Beijing seized it from Manila in 2012.

The newspaper said the one-day submarine exercises were Tokyo's first in the South China Sea.

The Maritime Self-Defence Force carried out a "practical" anti-submarine drill, including an exercise to spot enemy submarines with sonar devices, the Asahi said, quoting government sources.

The sources described it as a legitimate naval exercise in neutral waters, with rights of access under international law.

Abe stressed that he agreed with Chinese President Xi Jinping earlier this month that he will visit Beijing soon, saying Japan-China relations have entered "a new stage."

Chinese foreign ministry spokesman Geng Shuang declined to confirm the drill, but said that "the situation in the South China Sea is improving."

Japan "should act cautiously and avoid doing anything which would harm regional peace and stability", he told a regular press briefing.

Following the drill, the Japanese submarine made a port call on Monday at Cam Ranh in central Vietnam to promote defence cooperation with Hanoi, Japan's defence ministry said in a separate statement.

The submarine with 80 people aboard will stay until Friday.

It was the first call by any foreign submarine at the strategically important port, a defence ministry spokesman said, citing a Vietnamese counterpart.

China has engaged in years of land-reclamation work on reefs it controls in the South China Sea and has built both civilian and military facilities on them.

Earlier this month Beijing lashed out at Britain for sailing a warship close to the disputed islands -- one of a series of "freedom of navigation" exercises carried out in recent years by the US and its allies.