The train was heading from Yala, one of three Muslim-dominated provinces which have been the focus of the uprising in the region which flared in January 2004, to Hat Yai, the commercial centre of the south.
No trains would run south of Hat Yai until the track inspections, which were expected to be completed on Wednesday, Tanongsak Pongprasert, another rail official, said.
"We have had to suspend all 18 train services from and to Hat Yai today as we have to check the damage to the tracks and take the derailed train out of the way after the sabotage," he said, adding that "if there's no major hassle" service should resume on Thursday.
The Thai government has sent 30,000 soldiers to the south, but they have so far failed to end the near-daily violence that has killed more than 2,100 people since 2004.