He is under pressure from the United States to fully investigate the deaths of 78 Muslim protesters who were reported to have suffocated while in army custody.
Thaksin has defended the actions of his troops but admitted mistakes were made.
Hours before the security meeting in Bangkok on Thursday, police defused a fertiliser bomb, weighing nearly 4.5kg and packed in a plastic box, in Narathiwat town, scene of Monday's protest.
The prime minister, facing fierce criticism at home and abroad for his iron-fisted tactics, was due to meet security advisers at 2pm (0700 GMT), officials said.
The Committee of Security and Strategy, a group of senior generals and other officials, was set up earlier this month to advise Thaksin on major security threats.
"The unrest is not yet over and it might become more serious," former southern army commander General Kitti Ratanachaya told Thai daily The Nation.
Seventy-eight Muslim protesters
died on Monday in police custody
"Despite many months of unrest, the state authorities still don't understand that the problem stems from separatists," he said.
Muslim leaders have warned of a violent backlash to Monday's tragedy when 78 protesters suffocated as they were crammed into overcrowded trucks and driven five hours to a military base in Thailand's volatile south.
Seven others died in clashes as police tried to disperse the protest outside the Takbai police station in Narathiwat.
It was the worst violence in the mainly Muslim tip of the otherwise Buddhist kingdom since 28 April, when troops and police shot dead 106 machete-wielding Muslim fighters. The region is home to most of Thailand's six million Muslims.
Full probe demanded
As grieving relatives prepared to bury their dead, Washington urged Bangkok not to exacerbate tensions in a region where 440 people have died in a wave of violence since January.
"Thai authorities are responsible for the humane treatment of prisoners and we urge that their current investigation fully examine the circumstances of these deaths," US State Department spokeswoman Susan Pittman said in Washington.
Thaksin said a committee would "study lessons" from the incident, which he said was an accident because too few trucks were available to transport the more than 1200 protesters detained after the protest.
Relatives of the deceased are
preparing to bury them
However, no one would be punished, he said. Rights groups say the proposed committee falls far short of a full and independent judicial or legislative inquiry.
The Asian Human Rights Commission said it feared the committee "may be hastily established under the control of regional administrative officials with instructions to dispose of the matter as quickly as possible".
Meanwhile, a Philippine presidential spokesman said the death of the protesters was "unfortunate".
"It's unfortunate that such a thing happened. But again, we do not wish to really comment on incidents that are happening in other countries," spokesman Ignacio Bunye said.
Manila, which hopes to start peace talks next month with the leaders of a decades-old Muslim separatist rebellion in the south, rejected comparisons with sectarian tensions in the mostly Roman Catholic Philippines.
Bunye said the national government was letting local officials
and homeowners associations deal with a high-profile quarrel over a developer's plan to put up a Muslim prayer room at a suburban Manila shopping mall.