It is reportedly the first such ruling since the coast guard warned last year that the number of Chinese fishing boats hunting red corals had swelled in waters off Ogasawara, also known as the Bonin islands, in the Pacific far south of mainland Japan.
Red corals are highly prized in China as jewellery.
The Kagoshima district court in southwestern Japan issued a suspended 18-month jail term and three million yen ($25,000) fine against the 34-year-old skipper from China’s eastern Anhui province on Monday, after he was caught poaching in mid-November.
Presiding judge Naoyuki Yamada described the poaching as “extremely heinous because it destroyed precious coral resources that take a long time to recover from damage”.
A verdict in the case of another Chinese boat captain on similar charges is expected later Monday.
The number of Chinese boats in the area surged to more than 200 in October, a coastguard spokesman told AFP on Monday, but added that the figures have since declined after Japan jacked up fines for illegal fishing in its waters.
Last month, Japanese authorities said they had laid coral-poaching charges against crew from a record 16 Chinese vessels in 2014.
The maximum fine for poaching in territorial waters tripled in November to 30 million yen.
The Japanese coastguard tends to chase off Chinese crews hunting corals in the area and the incidents rarely cause major friction between Tokyo and Beijing, although they remain at loggerheads over ownership of an island chain in the East China Sea.
In October, the South Korean coastguard shot and killed the Chinese skipper of a fishing boat in a confrontation in the Yellow Sea, triggering an angry protest from Beijing.