"Persons who plan to visit Thailand now are warned not to travel to Patani Raya region... and the neighbouring provinces (Phuket, Pangnga, Krabi, Pattalung)," a statement by separatist group Bersatu said on Thursday.
"Patani people are not responsible for anything happens to you after this warning," it said in English, without elaborating.
The warning covers the top resort islands of Phuket and Phi Phi, the popular Krabi and Phang-nga regions and the five Muslim-majority provinces lying near Malaysia which are popular with tourists from over the border.
It came a day after 113 people including 108 young rebels were killed when they mounted raids on police stations and checkpoints in the southern provinces bordering Malaysia.
The statement was posted on an Internet site run by the Pattani United Liberation Organisation (PULO), which issued a call to arms to Muslims living in the south where an insurgency has been waged sporadically for four decades.
"We are calling all of you to rise up against the Siamese (Thais)," it said, claiming the government's treatment of the region since it was annexed a century ago amounted to "terrorist acts".
"Patani people are not responsible for anything happens to you after this warning"
Government spokesman Jacrapob Penkair said the warning was being analysed to determine whether it represented a serious threat.
"We will not panic over every bit of information posted on the Internet," he said.
Lieutenant General Jumpon Munmai, chief of the National Intelligence Agency, said authorities had been closely monitoring sites run by outlawed groups and vowed to take immediate action.
"They have frequently used this website in negative ways to incite unrest," he said. Thai internet providers appeared to have blocked access to the site.
Bersatu is an umbrella organisation which coordinates and represents separatist movements operating in the region. All have been banned by the Thai government.
PULO was a major force in the Muslim insurgency which raged in the south until the 1980s when a government campaign largely ended the movement, substantially weakening the separatist groups.
The last major attack it claimed responsibility for was an April 2001 bombing at the main southern train station at Hat Yai which killed one child and injured 37 others.