Gen Prayuth's call followed the latest spate of violence in the far South over the weekend resulting in the deaths of at least two soldiers and injuries to more than 10 people, including a nine-year-old girl.
The army chief conceded that local residents still resist cooperating with security agencies in dealing with rebels.
Soldiers are trying to reach an understanding with locals, he said, calling on other agencies involved to help find a solution to the conflict.
"Today, I am asking 17 ministries and 66 agencies concerned to help," he said. "Soldiers and police are only enforcing the laws. Without help from other agencies, it is hard to achieve understanding with local people."
Southern rebels launched the most recent attacks to show they are still a force to be reckoned with, he said.
Security agencies analyse the situation daily to predict where violence may occur, he added.
Prime Minister Yingluck Shinawatra yesterday expressed concern over the latest spate of southern violence and ordered all agencies involved to monitor the situation closely.
The government has agreed to increase the number of police officers and defence volunteers to support security operations in the lower South, Ms Yingluck said following a cabinet meeting on Koh Samui, Surat Thani.
The prime minister said she ordered Deputy Prime Minister Yutthasak Sasiprapa to resolve the southern violence, and told Gen Prayuth to travel to the southern border provinces today to analyse the situation and oversee local security operations.
Ms Yingluck said she wants to visit the far South to boost the morale of security officers and local residents, if time permits.
National police chief Adul Saengsingkaew yesterday arrived at the southern border police operations centre in Yala's Muang district to follow up on the attacks in Narathiwat in Tak Bai and Bacho districts over the weekend.
Pol Gen Adul said he ordered police officers to step up efforts to investigate and track down the attackers and bring them to justice.
Navy chief Adm Surasak Rounroengrom said yesterday the navy promoted the two officers attached to the navy's marine corps, who were killed in a bomb blast in Bacho district Saturday.
Petty Officer 1st Class Nadi Champawan was promoted to a commander and his family will receive more than 2.4 million baht in compensation while Petty Officer 1st Class Issarawut Polsak was promoted to a lieutenant commander and his family will receive about 2.1 million baht in compensation.
Adm Surasak said navy officers deployed in the lower South are ready to sacrifice their lives and their overall morale remains high. He said officers are always adjusting their tactics to suit the circumstances, he added.
Meanwhile, Foreign Minister Surapong Tovichakchaikul said during his visit to Egypt yesterday that Egypt's top Muslim cleric Sheikh Ahmed El-Tayeb had condemned the violence in the lower South.
Mr Surapong said he had submitted a letter on behalf of Ms Yingluck to invite the Egyptian spiritual leader to visit Thailand and he had already accepted. The visit is scheduled tentatively for next month.
Violent attacks continued yesterday in Pattani and Narathiwat.
In Pattani's Muang district, Somchai Homklinchan, 39, a gardener at Thanyarak Pattani hospital, was riding a motorcycle to work and was followed by two assailants on another motorcycle before a pillion-riding gunman shot him. The man was taken to a nearby hospital where he died.
In Narathiwat's Si Sakhon district, Sukanya Permsap, 50, the owner of a grocery, was shot dead in his shop. Soldiers and police were at the scene when militants hiding nearby detonated an explosion by radio signal. Nobody was hurt.
Security officers found Sukanya's body in the shop after the explosion. She had been shot in the head. A bomb crater marred the shop.
Debris was strewn about the shop including remnants from the homemade bomb. A pistol and a spent bullet case were also found.
Pol Col Kowit Rattanachote, Si Sakhon police chief, said the attack was believed to be the work of insurgents who planned to kill security officers.
However, security officers escaped unharmed because they have become familiar with attacks using similar strategies.