The commando, who belongs to South Waziristan Agency, was arrested for his links with the Taliban and al-Qaeda affiliates, The News daily quoted its sources as saying.
He was posted at PNS Mehran, the naval air station in Karachi that was stormed on Sunday by terrorists who killed 10 security personnel and destroyed two maritime surveillance aircraft.
Four of the attackers were killed or blew themselves up while two escaped. Besides disclosing details about the impending attack on the naval airbase, he had warned that oil depots and power grid stations were on the hit list of militants.
The commando, who was picked up because of his involvement in suspicious activities, had predicted attacks on other naval installations, said an unnamed official privy to the details.
No serious measures were taken to avert the attack on the naval airbase, the report said.
The Pakistan Navy's Directorate of Public Relations offered no comment on the matter.
The arrested commando is a member of the Mehsud tribe, which has produced Taliban leaders like Baitullah Mehsud, Qari Hussain, and Hakimullah Mehsud who have carried out a wave of bombings and suicide attacks across Pakistan.