Deputy Defence Minister and army commander Udomdej Sitabutr says the three-day bomb attacks across Yala, which have injured 22 people, are probably connected to political groups.
Gen Udomdej said he wants to wait for the results of police investigations into the latest violence and does not want to jump to conclusions.
However, he cannot help but see political issues as a possible motivation for the attacks, which took place between Thursday and Saturday.
"I don't want to say whether the problems involve local politicians with links to mainstream politics," he said Sunday.
"Local politicians, on the one hand, say they want to help restore peace, but on the other, provide support for perpetrators of violence to erode the government's credibility."
He made the comments before travelling to Yala yesterday to discuss the 36 bombings with security officers and plan stricter safety measures to avoid a recurrence of the blasts.
Gen Udomdej said local political problems, along with drugs and human trafficking, complicate the southern insurgency, which involves separatist groups based mainly in the Muslim-dominated provinces of Yala, Pattani and Narathiwat.
"Politics, the trade in humans and different ideologies are all interrelated," he said.
"Everyone says they love the nation and want to restore peace, but when conflicts with their personal aims arise, they choose to support the insurgent groups."
The problems cannot stop government's plans to restore peace in the deep South, he said.
In response to the Yala bombings, officers will strive to ensure cooperation between officers and villagers to ensure communities remain vigilant to attacks, Internal Security Operations Command spokesman Col Banpot Poonpian said after Gen Udomdej's meeting.
Police are currently tracking down their suspects. The officers have identified the attackers' group, deputy national police chief Chakthip Chaijinda revealed yesterday, without giving details.
The investigators believe there was a hidden agenda to the suspects' attacks because they planted many bombs near electricity posts, apparently to make them fall and cause a blackout.
Fortunately, a blackout did not occur, Gen Chakthip said.
The bombings caused widespread damage to assets, initially estimated at 10 million baht.