The Internal Security Operations Command (Isoc) has rejected a proposal by a Narathiwat teachers' group to transfer Buddhist teachers out of high-risk schools in the far South.
They said people with different religious beliefs should be able to live together.
The proposal was raised by the Confederation of Teachers in Narathiwat on Wednesday. It followed the shooting of two teachers in the province this week.
Gen Udomdej Sitabutr, army chief of staff and secretary-general of Isoc, said yesterday the agency was concerned by the proposal.
The transfer of Buddhist teachers was not possible, Gen Udomdej said, as Thailand should be a place of religious tolerance where teachers of all faiths are able to work without fear of persecution.
The Isoc secretary-general said security measures for teachers will be boosted, although this would require cooperation from security officers and teachers. The two sides have talked about how to approach security arrangements in the area, he said.
Gen Udomdej said Isoc had instructed its 4th Region Forward Command to work closely with other organisations to tighten security in the far South.
Meanwhile, Education Minister Pongthep Thepkanchana yesterday promised to look into teachers' requests to increase their welfare and other benefits.
The requests include bumping up the 2,500 baht hazard pay bonus by an extra 1,000 baht for teachers in the far South.
The requests will be put before cabinet, Mr Pongthep said after meeting 1,500 teachers from the three southernmost provinces in Pattani yesterday.
Mr Phongthep also yesterday attended the funeral of Chatsuda Nilsuwan, the 33-year-old teacher from Ban Ta-ngo school who was gunned down on Monday.
The funeral was held at Wat Walukaram in Muang district of Yala.
Chatsuda was shot and killed in Cho Airong district, Narathiwat, where her school was located.
The next day, 52-year-old Thirapol Chusaongsaeng a teacher at Ban Boko school, was shot and injured in the same province.
The shootings prompted the Confederation of Teachers in Narathiwat to suspend classes at 378 schools in the province.
Mr Pongthep called on teachers to have confidence in the government's security measures.
He said schools are expected to resume classes on Tuesday.
Mr Pongthep said schools throughout the deep South will be encouraged to teach in Thai, English and Melayu to bolster language proficiency for the introduction of the Asean Economic Community in 2015.
Boonsom Thongsriprai, chairman of the Confederation of Teachers of the Three Southern Border Provinces, who also attended the meeting, said he was was satisfied with the minister's visit to the region.
He said teachers did not want to close schools, but needed the authorities to take better care of teachers' safety instead of just focusing on who should be blamed for the violence.