Acting on a tip-off, the security forces raided a building in Harnai district and arrested the three suspects, police said.
A police official confirmed the arrests and said that the militants were shifted to a secret location for interrogation.
Weapons and explosives were also recovered from the militants, who were apparently planning to carry out a terrorist attack.
Pakistan has increased intelligence-based operation against militants following the Taliban attack last month on an army-run school in Peshawar which killed 150 people, mostly children.