The government said the schools were used as bases to launch attacks since January and hinted at harsher measures against rebels who had targeted Thai Buddhists, security officials and civil servants.
The government said fewer than 20 schools had connections to the rebellion, but warned that teachers who preached separatist messages to pupils faced a six-month jail term and fines of up to 50,000 baht ($1,220).
The Islamic schools at the heart of the dispute were all in the three worst-hit southern provinces of Yala, Narathiwat and Pattani.
The government said it was also considering cutting funding to some of the Islamic schools in a country that is overwhelmingly Buddhist.
Back to life
"There are fewer than 20 schools which have been involved with the uprising against the authorities in those three southern provinces, particularly in Narathiwat," Prime Minister Thaksin Shinawatra said on Tuesday after a cabinet meeting in Bangkok.
Violence peaked on 28 April when
rebels fought Thai security forces
"Of those, two schools would be shut down following the clear evidence," he said.
A separatist movement raged in Thailand's south until the 1980s to try to secure a homeland for Thai Muslims, but it fragmented and attacks dropped off.
However, the fighting sputtered back to life early this year when a raid on an army weapons depot left four soldiers dead.
The violence reached a peak on 28 April when 108 suspected Muslim rebels were killed when they launched raids on police posts and checkpoints.
Pattani was the scene of the latest killing on Tuesday when Tuanden Yuema, 32, a security volunteer, was shot dead by two attackers as he travelled to work by motorbike.
"We have to adjust our military strategy since they have killed two or three of our people daily," Thamarak Issaranggura Na Ayutthaya, the deputy prime minister, said.
"There are fewer than
20 schools which have been involved with
the uprising ..."
Thai Prime Minister Thaksin Shinawatra
Thai authorities have been accused of heavy-handed tactics to quell violence in the deprived south, including unwarranted detentions and excessive interrogations.
The government's latest initiatives have included pledges to pump money into the region, trying to create a national unity through a football tournament, and low-key talks with the rebels.
Bhokin Bhalakula, the Thai interior minister, on Monday said he would meet his Malaysian counterpart in August to ask for more help to track down the rebels.
The government has said some of the separatists operate out of Malaysia and drift across the porous border to launch attacks in Thailand.