Government spokesman Thanakorn Wangboonkongchana said Prayut received a report of the bomb attack, which injured four patrolling rangers and two civilians in front of a school in Bannang Sata district.
The PM also ordered authorities to tighten security around transport routes including the railway and roads in the area.
Meanwhile, Yala Governor Pirom Nilthaya was instructed to visit the injured in hospital and their homes.
Prayut also ordered tighter security plans and measures in every area, especially vulnerable points.
The spike in clashes between security forces and insurgent combatants comes after the government restarted peace talks with the separatist Barisan Revolusi Nasional (BRN) group earlier this year.