A Chinese fisherman was killed during the Coast Guard's crackdown on his ship's illegal fishing in South Korean waters Friday, officials said.

The 45-year-old 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.

"He died at Mokpo Hangook Hospital around 11:20 a.m. An autopsy is underway to determine the exact cause of his death," an official told Yonhap News Agency.

The Coast Guard used guns during the raid as Chinese fishermen on board fought with the Coast Guard officials, the officials said.

"The cause of Song's death is presumed to be the penetrating injuries sustained from a bullet," said Jeong Jong-hyun, an emergency doctor at Mokpo Hangook Hospital.

"The piece of bullet about 1.6 centimeters was found inside Song's body," Jeong said, citing a CT image.

Expressing regret over the incident, the Seoul government said it has explained the details of the incident to China through diplomatic channels.

Seoul's foreign ministry told China's counterpart that an investigation is underway to determine the exact cause of the incident, expressing regret over the death, according to an official at the ministry.

The Chinese government, meanwhile, expressed strong discontent over the incident.

"I heard of the incident this morning. It is really regrettable, and I am really sad," the consulate general of the People's Republic of China in Gwangju told reporters.

In Beijing, China's foreign ministry spokesman Hong Lei expressed a strong complaint over the incident, saying the Chinese government immediately lodged a protest with South Korea.

China also asked South Korea to thoroughly investigate the incident, Hong told reporters during a regular press briefing.

Chinese fishing boats have been repeatedly crossing into South Korean waters in the Yellow Sea in search of abundant fishery resources, often leading to violence by the Chinese crews during raids by the South Korean Coast Guard.

The Coast Guard arrested 183 Chinese fishermen in 2013 for illegal fishing in the Yellow Sea, according to the Coast Guard. (Yonhap)