Boonsom Tongsriplai, the head of the region's teachers' association, said that Pattani province's 332 schools would be closed indefinitely until officials could boost teachers' confidence in their security. He said teachers in Narathiwat and Yala provinces would be asked to join the boycott.
A female school principal was killed last on Thursday in Pattani's Nongchik district, the latest of scores of teachers targeted by the insurgents.
Narathiwat, Yala and Pattani are the only Muslim-majority provinces in Buddhist-dominated Thailand. More than 5,000 people have been killed since an Islamist insurgency flared in the three southernmost provinces in 2004.
The army tries to protect teachers by escorting them in convoys to and from school, and the soldiers are sometimes ambushed themselves. There are 1,305 schools in the three provinces.
Teachers are apparently targeted because they are symbols of the state and to make normal life difficult for Buddhist residents of the area so they will move away.
Boonsom said the teachers were sorry to inconvenience students and their parents, but were under stress from fear.
He said that when the issue was resolved and school reopened, teachers would offer extra classes to make up for the lost days.