Thai authorities and Muslim rebels leaders have started peace talks aimed at ending almost a decade of unrest in the country's far south, as fresh violence killed at least five people.

The talks on Thursday with representatives from the Barisan Revolusi Nasional (BRN) insurgent group, expected to last one day, will focus on reducing bloodshed, Thai National Security Council chief Paradorn Pattanatabut said, warning the overall peace process would take time.

"Today's main focus is to reduce violence. Today we will focus on building mutual trust and good relations," Paradorn told reporters in the Malaysian capital of Kuala Lumpur, where the meeting was being held.

Ahmad Zamzamin, a former senior aide of Malaysian Prime Minister Najib Razak, is facilitating the talks.

Prior to talks, a roadside bomb exploded in the Chor Ai-rong district of Narathiwat province, 840 kilometres south of Bangkok, killing three soldiers who were patrolling the area, said the 4th Army Region commander, Lieutenant General Udomchai Thammasarorat.

"The people of southern Thailand have become used to violence with attacks by suspected Muslim separatists happening on an almost daily basis," Al Jazeera's Wayne Hay said.

Five other soldiers were also wounded in the ambush.

Authorities say the attack took place in a village that is home to a key leader of the Muslim separatist group taking part in talks with the Thai government.

"We suspect this was the work of local militants who want to discredit the peace talks under way in Kuala Lumpur," Udomchai said.

A separate shooting incident was also reported in Narathiwat killing two Buddhist civilians.

The husband and wife were shot in Tak Bai district, where in 2004 more than 80 Muslim men died in a confrontation with security forces.

"That kind of underscores the difficulty of these talks," Al Jazeera's Florence Looi, reporting from Kuala Lumpur, said.

More than 5,300 people have been killed in the conflict in the majority-Muslim provinces in Thailand, which are under emergency law.

Rebels have carried out shootings and bombings on monks, teachers and village officials as symbols of the majority-Buddhist state.

In the past, Thailand and Malaysia have attempted, but eventually failed, to broker talks with the rebels.

"Analysts predict it will take many years before peace can be achieved in southern Thailand," Looi said. "It will be a long and arduous road. But many agree that Thursday's dialogue is a crucial first step".