About 50 militants attacked the unit in Narathiwat province on Wednesday evening, sparking a gun battle, Colonel Banphot Poonpien said.
"Four soldiers died in the attack and seven were injured. Of these, four are in a critical condition," he told AFP, adding that a number of weapons were stolen.
"It's unclear how many guns were taken by militants but they were mostly from dead soldiers," he said.
Suspected Islamic insurgents have waged a violent campaign in the southern region bordering Malaysia since early 2004, leaving more than 4,400 Muslims and Buddhists dead.
On Tuesday, Thailand extended emergency rule in most of the Muslim-majority southern region for another three months, despite rights groups' concerns about the powers awarded to the military.