The HTMS Sukhothai was patrolling the Gulf of Thailand, roughly 20 nautical miles from Bang Saphan pier in southern Prachuap Khiri Khan, when it ran into strong tides and took on water late Sunday night.
A rescue mission was launched after the vessel's electronic system was damaged, with pictures shared by the navy showing the ship dramatically heeling to one side.
"We are still looking for 31 missing," said navy spokesperson Admiral Pogkrong Montradpalin, adding that the ship sank shortly after midnight.
"The ship's operating systems stopped working, causing the ship to lose control," he said earlier Monday morning.
A statement said 75 of 106 personnel on board were pulled from the waters in a rescue operation involving two seahawk helicopters, two frigates and one amphibious ship.
The search-and-rescue operation, which started at 7 am, was ongoing, the statement added.
Around 11 naval personnel were being treated at Bang Saphan hospital, while some 40 others were being housed at shelters.