A 63-year-old store owner in Narathiwat province's Sukirin district was shot six times early on Sunday by a man posing as a customer, police said.
The killer fled on a motorcycle. The victim died on the way to hospital.
Late on Saturday, unidentified men sprayed a Buddhist shrine in nearby Yala province.
Another Buddhist man in his sixties was hit by two bullets and died at the scene, police said.
The Narathiwat shooting took place a few hours before Thaksin arrived at a temple in Tak Bai district, 70km away, for a donation ceremony and a meeting with security forces on the escalating violence.
The temple is near a police station where 78 Muslim protesters and bystanders suffocated after being heaped up in trucks while being transported to a military barracks.
"People should not fall into a trap since we know that some
groups want to create religious conflict," Thaksin said at Tak Bai. "The people in the south do not have religious disputes."
The Thai premier, accompanied by Defence Minister Sumpan Boonyanun, met southern business leaders earlier on Sunday before heading to Tak Bai for an hour-long visit.
It has come to light that seven Muslims protesters were initially killed in what police said were clashes during the demonstration on 25 October that ended in tragedy.
The Bangkok Post newspaper quoted the army commander in the south at the time, Lieutenant General Pisan Wattanawongkeeree, as saying some of the 85 Muslim protesters might have drowned.
He also stated that they were left face down on top of each other in water, with their hands tied behind their backs, while waiting to be transported to an army barracks for interrogation.
Rights groups and witnesses say
the army used excessive force
Prime Minister Thaksin had initially praised his security forces and said in his weekly radio address on Saturday he would urge security authorities to work more decisively in their operations to restore peace to the region.
Rights groups and community leaders have accused the government of dragging its feet and using excessive and disproportionate force.
More than 450 people have been killed since January.
In some incidents, the assailants left leaflets citing revenge for the deaths.
Thaksin, who flew back to Bangkok later on Sunday, has said the unrest may prevent him from joining re-elected US President George Bush and other Asia-Pacific leaders at a summit in Chile this month.