Gen Prayuth made his remarks this morning before boarding a plane to the southern border province to follow up military operations there.
He said the situation has improved in the deep South, adding that international organisations understand the situation and will not interfere.
Regarding the killings of Muslim community religious leaders, and Buddhist Thais who cooperated with state agencies, the army chief said the move was the insurgents' mistake as the victims are innocent people.
"Please stop attacking the people and the officials and return to dialogue," Gen Prayuth urgen. "The peace process will continue although it will take time."
Gen Prayuth also asked the public not to worry that Thailand will suffer a setback in the peace dialogue, saying that concerned officials have clear frameworks and principles on the issues.
The army chief said that the Internal Security Operations Command is now undergoing structural reform so that all agencies will work in a more harmonious way and using their budgets effectively.
Once the security personnel in deep South are strong enough to stand alone in their operations, Gen Prayuth said, additional troops coming from other regions will withdraw and return to their barracks.
Gen Prayuth urged all parties not to blame security personnel who work in deep South as it will discourage them.