As the four were flown from the predominantly Muslim south to the capital where a criminal court remanded them in custody, Prime Minister Thaksin Shinawatra said a suspect who eluded capture this week was behind the insurgency that has gripped the south this year.
Suspects Waeyuso Waeduramae, Muhamad Kanafi Doloh, Abdul Roseh Hayidoloh and Ahama Bula arrived at the court in vans escorted by armed guards, and were pushed through a crush of media crews and police, an AFP photographer said.
"They were remanded for 12 days for further interrogation, and they face six counts including treason and terrorism," a police officer told AFP. The charges carry the death penalty.
Police asked the Bangkok court to refuse bail, saying the four constituted a national security threat.
The four are "key mastermind figures" who had ordered the theft of government firearms and the attacking of officials and innocent civilians, Thai military officials said.
But in what could be seen as a blow to efforts to halt attacks, Thaksin identified a fifth suspect, Islamic school principal Sapae-ing Baso, as the mastermind of the insurgency, but he slipped the dragnet laid out this week in Yala province where the other four were caught.
Thailand's south has been gripped
by violence over the last year
"From the interrogations it has become clear that he, Sapae-ing, is the leader of the movement," Thaksin said.
The premier said another 100 key figures were being sought, most of whom he described as separatists, but said some of them may have fled the country.
Southern Thailand erupted in violence in January, and to date more than 560 people have been killed in shootings, bombings and other attacks as well as in security crackdowns.
Three people were killed in the south Wednesday, including a Buddhist village chief and a retired teacher. A police corporal was shot dead in Yala on Thursday night.