Thai troops are braced for new attacks after over 100 suspected militants were killed on Wednesday during fighting in the country's Muslim south.
The families of the victims have been burying their dead
Two extra battalions of soldiers have been sent to step up security.
Top generals have warned of a new military campaign by Islamists, but the prime minister said the attacks were carried out by criminal gangs.
Rights groups and some Muslim leaders have questioned the military's degree of force in quelling the attacks.
"Troops must be on maximum alert and well prepared for the second and third wave of attacks," said Defence Minister Chettha Thanajaro.
Bersatu, an umbrella group for separatists in the region, issued a statement warning visitors not to travel to Thailand's south.
"Patani people are not responsible for anything happens to you after this warning," the statement said, carried on the website of one of its member groups, the Patani United Liberation Organisation (Pulo).
The statement listed Thailand's Muslim-dominated southern provinces as well as tourist spots further north like Phuket and Krabi.
"I would say the military phase has just started," General Pallop Pinmanee, who presided over a bloody shoot-out at a mosque in Pattani on Wednesday, told Bangkok radio.
"Our current estimate is that the strength of their armed men and recruits is in the thousands," he said.
He said that it was "absolutely certain" the raids were mounted by Muslim separatists. Defence Minister Chettha said that it was possible "some of them were trained abroad".
Those who died were young and were mostly armed only with swords. But Mr Chettha said each group of attackers were led by a commander usually in his mid 30s.
"The leaders used AK-47 rifles, M-16 assault rifles to open the way for their men, who used only machetes," he said.
These comments are in sharp contrast to those by Prime Minister Thaksin Shinawatra and others in his administration.
Mr Thaksin dismissed the attacks as perpetrated by local "bandits", while the army chief, General Chaiyasidh Shinawatra, said many of the attackers appeared to be under the influence of drugs.
A leading Thai newspaper, The Nation, dismissed this explanation in a front page editorial on Thursday.
"What the two leaders do not see, or pretend not to see, is that this is not about addiction or banditry; this is about a fanatical ideology that none of us knew existed on such a grand scale," it said.
In the south, families of the victims gathered at army camps on Thursday to collect the bodies and rapidly bury them, in accordance with Muslim tradition.
The violence began before dawn on Wednesday as groups of young men launched apparently co-ordinated assaults on security posts throughout Yala, Pattani and Songkhla provinces.
But the security forces, who had been tipped off, were lying in wait and responded with devastating fire power, losing only five of their own men.
At least 30 of the attackers fled to the Krue Se mosque in Pattani. After a stand-off of several hours, the security forces stormed the building, killing those sheltering inside.
As another of the attackers died overnight, their official death toll was raised to 108.
New York-based Human Rights Watch said on Thursday that Thailand should launch an investigation into whether "such a high level of lethal force was necessary".