Japan China territorial tensions
A Chinese Coast Guard vessel is pictured on the disputed region of South China SeaErik De Castro/Reuters file photo

A sophisticated Chinese naval vessel has briefly sailed into Japanese waters while shadowing a US aircraft carrier in the region. Tokyo said the Chinese spy ship was spotted by one of its patrol aircraft.

Japan's defence ministry has launched an investigation into the matter and said it is probing the intention of the Chinese vessel, which entered the waters of Kuchinoerabu Island in south-western Japan.

Speaking to reporters, Deputy Chief Cabinet Secretary Hiroshige Seko said the intelligence ship was spotted at about 3.30am local time as it drifted in the Japanese territorial waters for about 90 minutes. The last time a Chinese warship entered Japan's waters was in 2004.

The Chinese ship was thought to be shadowing the John C Stennis aircraft carrier, which is in the region for joint naval exercises with Japan.

"The government will continue to take all possible measures for warning and surveillance activity for our territorial waters and airspace," Seko told reporters, according to Japan Times.

The incident comes within a week of a similar encounter in which a Chinese frigate was seen sailing close to a heavily disputed region in the East China Sea. Japan had summoned the Chinese envoy to Tokyo to protest against the incident.

The two Asian economic heavyweights have engaged in territorial row for several years over a disputed chain of islands in the East China Sea. The relationship between Tokyo and Beijing began to sour in 2012 after both countries stepped up their claims on the islands in the East China Sea and Japan purchased them from a private owner.

Beijing is also involved in a territorial battle with multiple nations over its unilateral claims on the South China Sea region.