"We will release those who are not involved. We just wanted to question them about recent activities at the school and in the area," Chamlong said.
"No one was injured in the raid that was carried out by more than 200 police and soldiers."
The military can search and detain suspects for interrogation for 30 days without charge under a state of emergency that has been in place in the region since July 2005.
More than 3,700 people have been killed in Thailand's three southernmost provinces since a separatist movement began in January 2004.
The provinces - Narathiwat, Pattani and Yala - are the only Muslim-majority areas in the mainly Buddhist country.
Muslims in the area have long complained of discrimination by the central government.
The region used to be an Islamic sultanate until it was annexed by Thailand in the early 20th century.