But the general said all state agencies involved must join hands to tackle the problem.
Gen Prayuth said Wednesday's visit to the South by Prime Minister Yingluck Shinawatra was a good sign as it reflected that the government was focusing its attention on the issue.
The army commander, however, said he did not know when the problem would be solved because the solution could not be achieved through military means alone.
"Globally, this kind of problem cannot be 100% solved," said Gen Prayuth. "The military is not the sole unit responsible for the problem."
He said past measures introduced by the government to fight the southern unrest have failed to effectively tackle it because there were many state organisations involved in the work.
He said the performance of state agencies in solving the southern unrest should not be judged just by the statistics on violence.
Gen Prayuth agreed, however, that those agencies which failed to carry out their duties must work harder to improve their work.
The army chief said the southern conflict was not a normal problem since the perpetrators were willing to do anything to attract overseas attention and turn it into an international issue.
"I have emphasised that this is a domestic issue. We'll do whatever it takes to prevent foreign involvement," he said.
Gen Prayuth said Thailand did not need any foreign help to tackle the southern problem.
His comments came in response to the planned meeting between the chairman of the Organisation of Islamic Cooperation (OIC) and the chief of the 4th Army Region on Sept 18-19.
Democrat leader Abhisit Vejjajiva called on Prime Minister Yingluck to attend parliamentary sessions when the southern unrest was discussed.
Deputy Prime Minister Chalerm Yubamrung has urged Mr Abhisit and his party's southern MPs to join the government in talking about the southern violence today.
The Democrat leader insisted that the prime minister must also take part in the forum.
Meanwhile, attacks continued in the South yesterday.
In Narathiwat's Rangae district, a bomb went off in a rubber plantation on the Rangae-Cho Ai Rong road yesterday morning, seriously injuring rubber planter, Jiraporn Rattanapong, 41.
In the province's Muang district, Suthirak Kongsuwan, 37, and Hadiha Samae, 32, were also wounded in a drive-by shooting in the afternoon while travelling on their motorcycle on a road in tambon Bang Por.
Police found later that Mr Suthirak had an outstanding arrest warrant for a murder near Bang Nara Bridge in Muang district last month. He was then placed under arrest.
Officials yesterday also defused a bomb planted on the Tan Yong Mat-Tolang road in Rangae district.