The announcement was made as Thailand's Deputy Education Minister Suthum Saengpratoom met with teachers in Pattani province on Thursday who complained they were too scared to work and could not afford guards.
"We have adopted the new schedule because of the violent situation," said education ministry official Sunand Thepsri.
The start date for the region's 826 state and Islamic schools has been delayed from 3 May to 17 May.
The government said earlier this week that two extra battalions, representing some 1,000 men, would be drafted into the region to reinforce the military presence and that many would be assigned to guarding schools.
Dozens of schools have been torched and several students slashed in machete attacks since a fresh wave of violence erupted in the south in January, culminating in bloody clashes on Wednesday between separatists and security forces.
The attacks, and warning letters sent to schools targeting teachers and students, have forced classes to be called off on several occasions over the past four months.
Sunand said that three provinces were preparing a new curriculum for hundreds of Islamic schools which would be reviewed by the minister of education.
"The military believes Islamic schools are teaching young people to fight"
Some of Thailand's religious schools have come under criticism from analysts who say they are radicalising young Muslims and recruiting them into the separatist cause.
Security analyst Panitan Watanayagorn said a small number of Islamic schools, many of which are represented by the Pusaka foundation which governs institutions for young children, were responsible for fomenting unrest.
"About 20,000 students have studied under the umbrella of Pusaka of which about 500 to 1,000 radicals have emerged, dividing themselves (into groups) in the south," he said.
An education ministry official on condition of anonymity said the schools were being monitored closely by the government to determine if the claims were true.
"The military believes Islamic schools are teaching young people to fight," he said. "The ministry believes that's not true... but some teachers trained in the Middle East may be trying to convince students about separatism."
Meanwhile, people expressed sadness and anger over events on Wednesday. "The people are upset and angry," said Yosoff Samail, 60, head cleric at the central mosque in the provincial town of Pattani, where troops killed more than 30 insurgents inside.
"They want to know why the army killed those in the mosque. Why did they use heavy weapons? Why they didn't ask the chief Islamic leader what to do?" he said after Friday prayers attended by more than 1,000 faithful, many spilling onto the streets.