Boonyasidh Suwannarat, provincial governor of Yala province, said police had shot dead at least 45 people after a series of coordinated raids on police outposts on Wednesday.
The largely Muslim province of Yala is 1300km south of capital Bangkok.
In the nearby province of Pattani, the local police chief said at least 13 attackers had been shot and killed.
Several policemen and army officers were also killed in the clashes.
One soldier died in one of the Yala attacks, which were led by groups of at least 20 black-clothed men with guns, swords and machetes, he added.
In nearby Pattani province, rebels attacked at least three security outposts, killing one soldier, the police said.
Thailand’s three southernmost provinces have been hit by a wave of shootings, bombings and arson attacks that have claimed at least 60 lives since a January raid on an army barrack.
Despite a military clampdown in the region, which was home to a low-key separatist rebellion in the 1970s and 1980s, the violence has shown few signs of abating.
Bangkok blames the trouble on local gangsters exploiting disaffected local Malay-speaking Muslim youths.