The man, who was not identified by Pakistani officials, was nabbed during a search operation in Bogra area of Chaman, a town close to border with Afghanistan.
Paramilitary Frontier Corps (FC) conducted the search operation in a compound on the outskirts of the city where they recovered 21 kilogrammes of explosives and bomb-making instruments, Geo TV reported.
The intelligence officer has been shifted to an undisclosed location for further investigation, the report said.
Balochistan government spokesman Anwarul Haq Kakar said that the arrested foreign intelligence officer is currently under investigation.
Kakar claimed that the arrest of the Afghan intelligence officer is a "link in the chain of events" that started with the arrest of Kulbhushan Yadav, also from Chaman last month.
Pakistan has claimed Yadav is an officer of Indian spy agency RAW - a charge denied by India.