General Sondhi Boonyaratkalin, who led the bloodless coup against the government of Thaksin Shinawatra, the Thai prime minister, on September 19, said that officials from several rebel factions had contacted army commanders and requested talks.
"I have agreed to the talks," Sondhi was quoted by AP news agency as saying.
"I stress that these will be talks, not negotiations. If they are seeking co-operation with us, that kind of approach is OK with me."
However Lieutenant-General Viroach Buacharoon, the region's most senior commander, said that contact was still in the early stages and only between lower level officials and intermediaries for the various groups.
He also said that the groups had to prove that they were serious about committing to talks by declaring a ceasefire.
"Before any dialogue takes place, the insurgents must stop the violence for a month to show their sincerity," he said.
Thaksin's government, which rejected holding talks with Islamist groups in the south, had been criticised for its forceful approach to the violence.
Thailand's Islamist separatists have been active in the south since the 1970s, but violence erupted in the region in January 2004 after a raid by fighters on an army barracks.
Islamist fighters then began a campaign of violence against authorities in the south, which led to a harsh response from Bangkok.
Hundreds of people have been killed in the violence, most recently in September when four people, including a Canadian tourist, died after bombs planted by separatists exploded in Thailand's commercial hub, Hat Yai.