A Chinese naval vessel was spotted entering Japanese territorial waters near the southern Kuchinoerabu island at around 6:00 am Saturday (2100 GMT Friday) and exiting southwest of Yakushima island nearly two hours later, the defence ministry said.
Following the incident, the foreign ministry "issued Japan's strong concern and protest" to China's embassy in Tokyo.
The ministry took "into account the past activities of Chinese naval vessels and others in the waters around Japan, and the recent intrusion into Japan's territorial airspace by a Chinese military plane," it said late Saturday.
Japan on Monday scrambled fighter jets after a two-minute incursion by Chinese Y-9 surveillance aircraft off the Danjo Islands in the East China Sea, which Tokyo slammed as a "serious violation" of its sovereignty.
China's growing economic and military clout in the Asia-Pacific region and its assertiveness in territorial disputes -- most recently with the Philippines -- has rattled the United States and its allies.
Last week, Japan's defence ministry sought 8.5 trillion yen ($59 billion) for the next fiscal year, its largest ever initial budget request, as part of the country's five-year, 43 trillion yen defence buildup plan through March 2028.
The request includes funding for so-called standoff capabilities to strike distant targets with missiles and unmanned vehicles.
It is higher than the ministry's 7.7 trillion yen initial request last year, but smaller than the actual budget of 9.4 trillion yen approved for the current fiscal year.
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