A senior Chinese diplomat has held an "emergency meeting" with South Korea's ambassador to China and lodged a protest after the captain of a Chinese fishing boat died during a violent clash with the South Korean Coast Guard during a crackdown on illegal fishing.

Chinese Assistant Foreign Minister Liu Jianchao met with the South Korean ambassador to China, Kwon Young-se, on Friday night and made "solemn representations" over the incident, which happened

144 kilometers off South Korea's western coast earlier Friday, the Chinese foreign ministry said in a statement.

Liu told Kwon that South Korea must "conduct an immediate and thorough investigation into the case, punish those responsible and take measures to prevent similar incidents from happening again,"

Liu was quoted as saying in the statement.

Kwon expressed "profound regrets" and "deep condolences" to the family of the captain, according to the statement.

The 45-year-old Chinese skipper, only identified by his surname Song, was shot by a South Korean Coast Guard officer on the ship in waters near Wangdeung Island in Buan County, North Jeolla Province, and transferred to a hospital in the southwestern port city, where he later died, Coast Guard officials said.

The scuffle erupted as South Korean Coast Guard officers confronted the Chinese boat over illegal fishing.

According to the South Korean Coast Guard, the Chinese fishermen resisted violently with knives and beer bottles during the raid.

A South Korean officer fired shots from a K-5 pistol as warnings, but the shots were not specifically aimed at the captain, according to the Coast Guard.

In 2011, a South Korean Coast Guard officer was killed by Chinese fishermen during a raid against illegal fishing in South Korean waters. (Yonhap)