Owners, captains and crew now face fines of up to 20,000 baht and jail terms of up to five years.
Fishing vessels Bamrong Thai Nawa 18 and 19 were boarded by officials on a Phuket Marine Biological Centre boat just two kilometres off Patong overnight on July 1.
Held and charged were two Thais and nine Burmese on board, all arrested for fishing within the three-kilometre limit.
The Director of Marine Natural Resources, Paitoon Planchaiyabhum, said the tip-off that the Phuket-based vessels were fishing too close to shore came from another trawler.
''We sometimes have problems making raids because all the trawler fishermen know what the Marine Biological Centre vessel looks like,'' Khun Paitoon said.
''These two trawlers, though, have broken the law many times.''
He said the last arrest of trawler crew off Phuket had been about two years ago.