Muslims make up more than 90 per cent of the two million people in southern provinces of Yala, Pattani, Narathiwat and Songkhla.
Many complain of being treated as second-class citizens in mainly Buddhist Thailand.
The area was a semi-autonomous Islamic Malay sultanate until annexed by Thailand in 1902.
Several violent uprisings have been put down by the army over the century.
The latest uprising flared in January 2004 when fighters raided an army base, killing four soldiers.
Despite martial law imposed in 2004 and tens of thousands of military or paramilitary troops in the region, frequent attacks blamed on Muslim fighters have left more than 3,700 people dead.
No suspects were taken into custody or were known to have escaped, police said.
They added that they were checking the identities of the dead but believed all - including Arhama Duramae Pa-do, suspected of shooting a policeman last year - were subject to arrest warrants.
Two rifles, one pistol and a hand grenade were found inside the house, according to the police.
More than 3,700 people have been killed in Thailand's three southernmost provinces since fighting flared in January 2004 and a massive security presence has failed to stem the violence.
The provinces are the only Muslim-majority areas in predominantly Buddhist Thailand and Muslims there have long complained of discrimination by the central government.
Fighters have targeted both Buddhists and Muslims they believe are working with the government.
They have also attacked civilians, a move some say is to scare the Buddhist community into fleeing.
But so far they have not targeted popular resorts and tourist spots located in Thailand's south.
The fighters have not specifically stated the reasons why they are fighting but local observers say they are thought to be seeking an independent Muslim state.