CTD has said that Ghulam Mohammad and Lal Mohammad were convincing the citizens to join Islamic State by distributing pamphlets.
The raid was carried out on an intelligence tip, CTD said.
The counter terrorism department also stated that the pamphlets were written in Persian and Pashto language.
Cases have been filed under the Anti Terrorism Act 1997.
The Islamic State group on Wednesday had claimed responsibility for an attack by gunmen on a bus that killed at least 43 Ismaili community members in Pakistan’s biggest city Karachi.