Officials said the soldiers were in a truck in Raman district of Yala province, 805 kilometres south of Bangkok, when they were blocked by a pickup truck at about 7 am.
As they approached, militants hiding nearby detonated explosives in the vehicle.
The insurgents stole five M-16 rifles and fled, Lt Gen Udomchai Thammasarorat said.
"We had been warning local authorities to be prepared for attacks by insurgents," he said. "We are on alert all the time, but today(the insurgents) had a chance and we failed to stop them." On Tuesday, four fruit merchants were shot dead in an attack police said was aimed at intimidating civilians and forcingnon-Muslims to leave the three Muslim-majority provinces of Yala, Pattani and Narathiwat.
The militants are seeking independence from predominantly Buddhist Thailand.
About 5,300 people have been killed in bombings, shootings, beheadings and arson attacks since the long-running insurgency intensified in 2004.dpa