The State Railway of Thailand said the line was now safe and normal service for trains to southernmost provinces resumed after the tracks were fixed.
Six border patrol police making a security check at 5am found the bolts had been removed.
Jaruek Wunchim, the team leader, said 200 bolts were missing between kilometre markers 989 and 990 and officers contacted officials at Hat Yai station to repair the line.
The missing bolts caused some delays for trains running between Hat Yai district and stations in Pattani, Yala and Narathiwat, the railway agency said.
Security authorities are investigating whether the removal of the bolts was simple thefts or whether they were removed by insurgents, said Pol Lt Col Jaruek.
The latter possibility is being taken seriously given the high security alert in the area ahead of the 10th anniversary of the Kru Sue Mosque attack on Monday.
The Krue Se incident began on April 28, 2004 when 32 suspected guerrillas took shelter in the mosque in Pattani's Muang district. After a seven-hour standoff with military personnel, soldiers attacked and killed all 32.
The attack was made in contradiction of orders from the defence minister to end the confrontation peacefully.
The Krue Se incident sparked the revival of a long-dormant insurgency movement and a decade of continuing violence that has taken nearly 6,000 lives.