They cover the provinces of Yala, Pattani and Narathiwat, where more than 3,000 have been killed since violence flared in 2004.
Southern Muslims accuse the central government of discrimination, especially in jobs and education.
They comprise the majority in Thailand's far south, while the rest of the country is mainly Buddhist.
Human rights activists have criticised the continued use of emergency rule, saying it violates constitutional rights and has failed to contain violence.
The state of emergency allows the government to impose curfews, prohibit public gatherings, censor and ban publications, detain suspects without charge, confiscate property and tap telephones.
It also gives officials legal immunity for acts - including killings - carried out under its provisions, the Associated Press reported.
One of the major groups associated with the separatist insurgency in southern Thailand said earlier this month it wants to work with the Thai government to find a peaceful solution to the fighting.
A statement posted on the Web site of PULO, the Pattani United Liberation Organization, on April 8 said the group "is fully committed to finding a peaceful resolution of the conflict".
The Thai government has avoided open negotiations with the rebels.