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The decree, which was first introduced in 2005 provinces of Yala, Pattani and Narathiwat, has been criticised by rights campaigners who say it effectively gives the army legal immunity.
The state of emergency allows the military to detain suspects for questioning without charge.
Suspected Islamic insurgents have waged a violent campaign in the region since early 2004, leaving more than 4,500 Muslims and Buddhists dead.
"There are still attempts to use violence to attack officials and innocent people," deputy government spokesman Supachai Jaisamut said.