Speaking after the bloodiest day in recent Thai history, Thaksin Shinawatra blamed local gangs for the violence.
Many were killed as they attacked security posts, while at least 30 died after taking refuge in a mosque.
But concern is growing that the government's response was heavy-handed and could spark more violence.
'Bandits'
The attackers were "youths from the southern provinces" whose actions were "not linked with international terrorists," the prime minister told reporters.
"We will uproot them, depriving them of a chance to allude to issues of separatism and religion. In the end they were all bandits."
Muslims in Thailand's poor southern provinces, where separatist tensions have simmered for decades, have long felt discriminated against by the government in Bangkok.
Many observers say the current troubles in the south have been exacerbated by the government's policy of cracking down on militants, using heavy-handed tactics that may have served to encourage those who already felt disenfranchised.
And some analysts have voiced concerns that Wednesday's attackers could have links to militant groups outside Thailand.
One of the men killed was found to be wearing a shirt with JI emblazoned on the back - a possible reference to Jemaah Islamiah, the group blamed for the Bali bombings.
Lying in wait
The violence began before dawn as groups of young men, many in their teens and armed with machetes and a few guns, launched apparently co-ordinated assaults on security posts throughout the Muslim-dominated southern provinces - Yala, Pattani and Songkhla.
At least 30 of the attackers fled to the Krue Se mosque in Pattani. After a stand-off of several hours, the security forces stormed the building, killing those sheltering inside.
The army chief, General Chaiyasidh Shinawatra, said many of the attackers appeared to be under the influence of drugs and a government spokesman, Jakrapob Penakir, insisted they were common criminals rather than trained terrorists.
"Judging from what we have seen tangibly, it seems like they haven't prepared that well for the operation this morning," he said.
Human rights activists have asked why if the authorities were warned, they could not arrest the attackers before the assaults began
Abdul Rosue Aree of the Islamic Council in nearby Narathiwat province said he feared the deaths could escalate the problems.
"The incident will definitely affect Muslim people's feelings. They will have bad feelings towards authorities and the turmoil will continue," he told the French news agency, AFP.
Thailand is predominantly Buddhist, with its 4% Muslim population concentrated in the troubled southern provinces - Pattani, Yala, Songkhla and Narathiwat.