Damage had not yet been assessed, Jalali said Sunday.
"All of the centers and apparatuses suspected of being infected with the virus are under control. The cyber defense base is working round-the-clock to adopt the necessary measures to counter cyberattacks and the infiltration of spyware," he told the IRNA news agency.
Duqu, a computer worm, gets its name from the "DQ" it gives to names of files it creates. It was discovered in September by the Laboratory of Cryptography and Systems Security at the Budapest University of Technology and Economics in Hungary.
It is thought to be related to the Stuxnet worm, which last year targeted Iranian computers linked to uranium facilities at the Natanz and Bushehr nuclear plants.