Abd al-Wahid Lari added some of the al-Qaida captives may have to be deported to the countries from which they entered Iran.
His comments came after Intelligence Minister Ali Yunesi confirmed senior members of the outlawed network were among many Iran was still holding after the US-led war toppled the Taliban government in neighbouring Afghanistan.
After a cabinet meeting, Yunesi told a press conference on Wednesday that Iran has already expelled and handed over many al-Qaida suspects to their native countries.
"Wherever we learn of some clues about people connected to al-Qaida, we launch intelligence operations and arrest them. We are firm on this because we consider it our duty to do so," Yunesi added.
The intelligence minister did not name any of the detainees, but there is speculation Iran is holding al-Qaida's number two, Ayman al-Zawahri, and the group's spokesman Sulayman Abu Ghaith and possibly even its security chief Saif al-Adil.
During an official visit to South Africa on Tuesday, Iranian Foreign Minister Kamal Kharrazi said Iran had never been harbouring terrorists but actively fighting against them.
His remarks came after US President George Bush accused Syria and Iran of continuing to harbour terrorists on Monday.
Last month, Tehran said it was holding talks with foreign intelligence services over the circumstances of detained members of the al-Qaida group.
Sabah Zanganeh, an adviser to Iran's foreign minister, said some of the detainees were Saudi nationals and Iran would hand them over to Riyadh.
The Saudi foreign minister visited Tehran in June to discuss the extradition of the Saudi detainees. Kuwait, however, has withdrawn citizenship from those detained and is not accepting al-Qaida suspects’ extradition.
Earlier this year, Iran said it had extradited more than 500 al-Qaida members to their homelands - including Arab, European and African countries.