Elite police led by intelligence agencies and backed up by paramilitary Rangers searched a compound in Tarnol area near Islamabad in the early morning swoop.
A police official said that a huge cache of arms and ammunition, eight kilograms of explosive material, detonators, and narcotics were recovered from them.
"We nabbed 59 suspects and shifted them to a secret location for questioning," he said.
Private media footage showed the weapons recovered during the raid.
The raid was part of efforts to eliminate militants, their financiers and facilitators from the country under the National Action Plan launched earlier this year.