The swoop on Monday at a house in Tarnol, in the city's southwest, also recovered fuses, detonators, wires and other bomb-making material, police said.
"They had several bags filled with explosives. They had wires and a complete system which can detonate the explosive," a police official told AFP, requesting anonymity.
Rab Nawaz, the officer investigating the case, confirmed the arrests and recovery of the explosives and told AFP that a case has been registered against the three accused.
"They had rented a house and had everything they needed to detonate explosives," Nawaz said.
A suicide attack on Monday in a market next to the military's headquarters had killed 13 people including eight soldiers and three children.
On Sunday, a vehicle-borne suicide bomb in Bannu had killed 26 members of the Frontier Corps, the deadliest attack on Pakistan's military in several years.
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