The officer, surnamed Lee, was killed Monday as his Coast Guard team clashed with the Chinese sailors while trying to seize the 66-ton vessel for fishing illegally in South Korea's exclusive economic zone in the Yellow Sea.
The Coast Guard believes the captain stabbed the 41-year-old corporal to death with two knives during the raid. Officials said they collected fingerprints from the knives found in the boat's steering house and sent them for analysis.
But the captain, 42, denied the accusations during an overnight interrogation, they said.
"We are investigating on the belief that the captain resorted to the second knife after wielding and dropping the first one," one Coast Guard official said.
"The Chinese captain has totally denied the crime ... but a postmortem on the officer showed that the depth of a cut matches the length of a knife (found on the scene)," Ahn Sung-sik, an official of the Coast Guard, said in a press briefing.
The captain also seriously wounded another Coast Guard officer.
Officials said they would seek arrest warrants later Tuesday for the captain on charges of murder and illegal intrusion of the country's exclusive economic zone.
They will also seek warrants for the eight remaining sailors to arrest and further interrogate them on accusations of obstructing government affairs, the Coast Guard also noted. The sailors admitted to their illegal fishing during their overnight interrogations.
Coast Guard officers also seized another Chinese fishing vessel carrying 10 sailors on suspicion of fishing illegally together with the first vessel. Officials said they are looking into suspicions that the vessel deliberately rammed the first boat to obstruct the raid operation.
Chinese fishing ships illegally cross into South Korea's Yellow Sea every year in search of anchovies, blue crabs and croakers, rich in the local sea. The intrusions spark frequent clashes with the Coast Guard, sometimes leading to deaths of local officers.
The Coast Guard said they have captured or sent back a total of 472 Chinese vessels so far this year for illegally fishing in the Yellow Sea.
The Coast Guard officer's death sparked outrage from South Koreans.
About 300 protesters, mainly from right-wing civic groups, gathered at the Chinese Embassy in central Seoul in the early afternoon. About 30 attempted to enter the embassy but were stopped by police.
A 34-year-old man was arrested after slamming his sports utility vehicle toward the embassy. His car crashed into a police bus surrounding the embassy building.
"I wanted to ram into a gate of the embassy at least, as a way of protest," the man identified by his surname Lee said as he was arrested.