Police and soldiers fought armed groups who launched dawn attacks at 10 locations in the three provinces of Yala, Pattani and Songkhla which lie near the Malaysian border.
"The attackers were mostly teenagers, and they targeted police and army checkpoints," said regional police commander Prung Boonpadung.
Major Chitnart Bunnothok, spokesman for the Fourth Army which patrols the troubled region, said 93 attackers were killed, 12 were injured and one was arrested.
"The toll is likely to go higher because we have not yet cleared all the areas," he said.
Low police casualties
Prime Minister Thaksin Shinawatra said only two security personnel were killed and that the toll was low because police and army were well prepared and the attackers were only armed with machetes and a few guns.
Security forces have suffered
Authorities said fighting was continuing at a mosque in Pattani province where rebels were holed up.
"We have sealed off the mosque in order to get them alive so we can question them and know their real motives," said Deputy Prime Minister Chavalit Yongchaiyudh.
The attacks were the latest in a series of bombings, raids and murders in Thailand's southern provinces, which over the past four months have claimed the lives of about 65 members of the security forces, government officials and Buddhist monks.
Deputy director of the Internal Security Command, General Panlop Pinmanee, said it was "absolutely certain" the rebels were separatists and they were trained by Muslim armed groups operating in the south.
Thaksin did not contradict Panlop's assertion that separatists were to blame, but downplayed the sectarian nature of the trouble, saying the militia responsible was made up of both Thai Muslims and Buddhists.
"I am really concerned that the problems in
the south will escalate even further"
Abd al-Rosue Aree,
deputy chairman, Islamic Council, Narathiwat
Islamic leaders said they feared Wednesday's unprecedented violence and the high death toll among the young rebels would spark a major deterioration in the south.
"I am really concerned that the problems in the south will escalate even further," said Abd al-Rosue Aree, deputy chairman of the Islamic Council in Narathiwat.
"The incident will definitely affect Muslim people's feelings. They will have bad feelings towards authorities and the turmoil will continue. It will not be resolved," he said.
Thailand is a predominantly Buddhist nation, but about 5% of the population is Muslim living mostly in the five southern provinces bordering Malaysia.
A separatist movement raged in the region until the 1980s until a government campaign largely ended the movement, but troubles have flared again in recent years, sparking fears that rebels had been mobilised by armed groups from abroad.