Since the attacks a week ago, Thaksin has consistently attributed the violence in the region to criminals, not Muslim separatists some aides say are responsible.
But on Sunday, Thaksin suggested there might be a link between Islamists and the raid on an army base and torching of 21 state schools a week ago that ignited fears of a separatist insurgency.
When asked by reporters if some private Islamic schools were being used to train militants, Thaksin said: "Of course. Our intelligence has to be better than this. We will not let them continue doing this kind of thing."
He said authorities would investigate the schools, but he gave no further details.
"There is no one above the law. We allow everyone to practice their religion freely. But everyone must also abide by
the law," he said.
300 Islamic schools
There are about 300 Islamic schools in southern Thailand, which is home to six million Muslims, or about 10% of the largely-Buddhist country's population.
Thaksin has dismissed statements by top aides that Islamists possibly connected to Jemaah Islamiah, the Southeast Asian network believed responsible for the nightclub bombings on the Indonesian island of Bali in 2002, were behind the attacks.
Police say Bersatu, which in Malay means united, is an umbrella organisation linking several separatist groups, including the Gerakan Mujahidin Islam Pattani, the Barisan Revolusi Nasional and Pattani United Liberation Organisation.
"There is no one above the law. We allow everyone to practice their religion freely. But everyone must also abide by the law"
Thai prime minister
Some of these are thought to have links to Malaysian groups which in turn have connections to Jemaah Islamiah. Some security experts say Jemaah Islamah is the southeast Asian wing of Usama bin Ladin's al-Qaida.
Thaksin promised on Saturday to deliver a new wave of development help to the three southern provinces put under
martial law after the latest violence.
The region is among the poorest in Thailand and has a history of conflict between Muslims and the security apparatus.
However, the intense manhunt by soldiers and a round-up of 300 suspects for questioning, including Islamic teachers, has fuelled resentment against the Bangkok government.
The army released a statement on Sunday, denying reports that soldiers had disturbed Muslim graves while searching a cemetery for guns stolen during the raid on the army base.
"The relationship between government officials and villagers is quite distant. They come to villages only when there have been incidents. They did not maintain a good relationship during normal times"
It said the soldiers had used metal detectors and remained outside the cemetery, located near the army base in Narathiwat province.
"There are people with bad intentions who want to sow dissent in the community by perpetrating baseless rumours," the army said.
"Some of these bad-intentioned people are trying to instigate and cause harm by using religion in order to cause further divisions between people who are working to improve the
situation in the south in line with the government's plan," it
Nevertheless, the security crackdown has deepened cracks between the Muslim community and government officials.
"Generally speaking, villagers did not like seeing their spiritual leader detained," Islamic leader Muhammad Hajiwesahak told Reuters, following his release on Saturday after two days of questioning by police.
"The relationship between government officials and villagers is quite distant. They come to villages only when there have been incidents. They did not maintain a good relationship during normal times," he said.