They said nine Chinese have been arrested for the attack on the four officials who boarded the 227-ton boat in the Yellow Sea near Heuksan Island.
One South Korean fell overboard after being hit with a club but was rescued, while three others sustained injuries to their heads, arms and legs. They were taken by helicopter to a hospital in the southwesten port of Mokpo.
"The Chinese sailors were seized while trying to escape. They are being taken to our base," a coastguard spokesman in Mokpo told AFP.
Seoul urged Beijing to take stronger action against illegal fishing after a Chinese skipper murdered a South Korean coastguard officer during an operation to stop illegal fishing last December.
The skipper was sentenced to 30 years in prison in April. Nine other Chinese crew members were given jail terms ranging from 18 months to five years.
It was the second time a South Korean coastguard had died at the hands of Chinese fishermen in less than four years and the incident sparked widespread public anger.
South Korea has announced plans to spend 932.4 billion won ($811 million) between 2012 and 2015 on better equipping its forces as part of a crackdown on poaching, including issuing more firearms.
It seized 475 boats last year compared with 370 in 2010.
When stopped, Chinese crews have often fought back with metal pipes and knives or lashed their boats together to deter boarders.