Thailand is to start peace talks with Muslim rebel groups operating in the south, a senior security official said on Wednesday, signaling a possible breakthrough in a conflict that has claimed over 5,000 lives.

The rebel groups have never clearly stated their demands since the insurgency flared up in 2004 but they are thought to want more autonomy or a separate state in a region that was part of a Malay sultanate until annexed by Thailand in 1909.

"This is the first step. The start of a peace dialogue with representatives from Muslim rebel groups," Paradorn Pattanathabutr, secretary-general of the National Security Council (NSC), told Reuters by phone from Kuala Lumpur.

An agreement on preliminary discussions is to be signed on Thursday in Kuala Lumpur ahead of a meeting between Thai Prime Minister Yingluck Shinawatra and her Malaysian counterpart, Najib Razak.

The two are due to hold a joint news conference.

Malaysia, which helped broker a peace deal between the Philippine government and Muslim rebel groups in October, appears to have brought the Thai rebel groups to the table.

Previous attempts at talks have gone nowhere and analysts said it was not even clear the participants in those talks were the legitimate leaders of the insurgency.

Before leaving for Malaysia, Paradorn had said Thailand would seek Malaysia's help to determine which rebel groups were operating in Thailand's southern provinces and then facilitate talks with the groups.

"There has been dialogue with insurgent groups on and off for many months but not as often as we would like," he said.

The NSC brings together government ministers and officials charged with coordinating security with the military. In a 2012 paper, it acknowledged a political dimension to the violence and proposed dialogue with the insurgents, but the military, which has a big presence in the south, is lukewarm.

Successive Thai governments and the military have made contact with rebel groups and claimed some success in tracking down key operatives but they have never held formal talks.

Thai authorities say the attacks in the south are organized by the Barisan Revolusi Nasional Coordinate, an offshoot of the Patani Malay National Revolutionary Front established in the 1960s to seek greater autonomy.

Another group, the Patani United Liberation Front, publicly calls for a separate state.

Reuters