
Indonesian Vice President Jusuf Kalla is mediating the talks in Bogor, about 60 kilometres south of Jakarta, presidential spokesman Dino Patti Djalal said.
Djalal said Indonesia would continue promoting peace in southern Thailand through its position as a facilitator for talks.
"The first meeting between the two sides has been concluded and has achieved some progress," the state-run Antara news agency quoted Djalal as saying.
"They agreed to exercise restraint to avoid any incidence that would undermine this peace process. They agreed not to commit any violence," the agency said.
Five representatives from Thailand's predominantly Muslim South and the national government in Bangkok participated in the two-day meeting, which ended on Sunday.
A number of important principles have been agreed upon although the settlement of some crucial issues still need mediation, Djalal said.
"What is important is that this process will continue. It was agreed that the conflict had to be settled peacefully and within the Thai constitution," he added.
The two sides have agreed to hold a second round of talks in Bogor on November 1 and 2, with a third session later in the month.
"We hope the talks would continue and develop in stages like in the peace process for Aceh. What is encouraging is that they have agreed to hold talks on politics and administrative systems in the second round," he said.
They will also be discussing defence, military, sociocultural, economic and educational issues, he said.
Since the latest violence erupted in Thailand's four southernmost provinces in 2004, the rebels have never revealed themselves publicly or claimed responsibility for the near daily gun and bomb attacks in the rubber-producing region bordering Malaysia.
Kalla was the driving force behind the 2005 Aceh peace agreement that ended three decades of conflict with separatists in the staunchly Muslim province on the tip of Sumatra.
The closed-door talks on the insurgent South were also attended by Indonesia's ambassador to Thailand and analysts.