Government pathologist Pornthip Rojanasunan told a news conference that she and a team of doctors conducted autopsies on 78 bodies at an army camp in Pattani province and found that most of the dead had perished from suffocation, according to Arabic news channel Al Jazeera.
"Seventy-eight people died from suffocation. We found no wounds on their bodies," senior justice ministry official Manit Sutaporn told a news conference in the southern town of Pattani.
They were among some 1300 people arrested on Monday following a riot in Thailand's Muslim-dominated southern provinces, which left six dead and dozens injured.
A similar day-long clash in April left 108 dead.
The violence erupted late on Monday after a six-hour demonstration held by about 2000 protesters outside a police station in Narathiwat province's Takbai district seeking the release of six security volunteers accused of giving their weapons to insurgents.
Thai police and military forces say they tried to disperse the crowd with gunshots, water cannons and tear gas canisters. Witnesses say the police fired live rounds into the air and at the crowd.
"The leaders and core members who created the riot will be put on trial and the unwitting followers will be released soon, but I cannot say exactly when," said Commander General Sirichai Thanyasiri, who heads a new task force to improve security in the southern provinces.
Prime Minister Thaksin Shinawatra, who rushed to the scene before returning to Bangkok late on Monday, insisted the crackdown was justified.
"We cannot allow these people to harass innocent people and authorities any longer," he said.
"We cannot tolerate these bad things any longer. The bad-intentioned people instigate the youths to create violence and chaos, so we have no choice but to use force to suppress them."
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