More than 10 assailants launched the attack on Aiyaweng police station in Yala province's Betong district after luring officers outside with a phone call, telling them of a fire at a nearby bridge, Major Jiarapan Kasemsansuk said.
"They attacked the police station in Aiyaweng area of Betong district for about 30 minutes," he said.
The assailants used M-16 rifles and two policemen received minor injuries when they were hit by pieces of cement during the firefight, said a policeman who was present at the station.
"Police are now in hot pursuit of the attackers," he added.
The attack came even as three senior ministers were scheduled to hold a second day of emergency talks with officials in nearby Pattani province after two days of violence left six people dead in the region.
Commander of Pattani police Major General Paitoon Pattanasophon said the assault was not linked to Sunday and Monday's violence, which included a brazen arms robbery at an army base, arson attacks on 18 schools and bomb plants.
A man rummaging through the
debris of a torched school
"This morning's situation in Yala was not connected to what happened here. It's another group," he told reporters.
Paitoon blamed local bandits for the bloodshed and said the situation was back to normal in the south.
"The situation is normal now. It's just general bandits, they're not involved in a separatist movement," he said.
The government has fumbled in attempts to finger blame for the attacks, with Thai Prime Minister Thaksin Shinawatra on Monday blaming people "tied to mujahidin" who were not separatists.
However, he backtracked later, saying that business conflicts were probably the root of the trouble.
Wake up call
Thaksin said on Wednesday the attacks were a "big wake up call" to the country's security forces.
"This incident shows our prolonged weakness in working together and in relations between officials and residents. It will be a big wake up call for the Thai security system"
Thai Prime Minister
Labelling the attacks as "regrettable", the prime minister said the government "must accept that we underestimated some things".
"This incident shows our prolonged weakness in working together and in relations between officials and residents," he said during a special lecture to students at the King Prachatipok Institute of political studies.
"It will be a big wake up call for the Thai security system and we must solve the problem systematically. It is a lesson for us."
A Muslim separatist movement has been raging for decades in Thailand's far south bordering Malaysia, but most analysts believe the groups have broken up and are in no position to launch such well-coordinated attacks.
Analysts have said the attacks were a marked departure from previous violence and could have been staged by organised crime gangs and militant groups working in tandem.