Foreign Ministry spokesman Masud Khan said Abd al-Qadir Khan was being questioned in connection with "debriefings" of several scientists working at his Khan Research Laboratories.
The minister however denied that the government had placed restrictions on Khan.
"He is too eminent a scientist to undergo a normal debriefing session," he said. "However, some questions have been raised with him in relation to the ongoing debriefing sessions."
This follows a report by the New York Times that information Iran turned over to the International Atomic Energy Agency two months ago has strengthened suspicions that Pakistan sold key nuclear secrets to Iran.
"American and European investigators are interested in what they describe as Iran's purchase of nuclear centrifuge designs from Pakistan 16 years ago, largely to force the Pakistani government to face up to a pattern of clandestine sales by its nuclear engineers and to investigate much more recent transfers," including ones to North Korea in the late 1990s, the Times said.
The investigation has led to the questioning of three senior nuclear scientists by Pakistani officials, the paper added.
US intelligence experts have been permitted to assist in the questioning, according to The Washington Post.
The Pakistani Foreign Minister denies the Post's report. "These are purely in-house investigations. No foreigners or foreign agencies are associated with the debriefing sessions in sensitive organisations", he said.
Pakistan's suspected role in providing centrifuge designs to Iran was first reported Sunday in the Post, which said the blueprints provided a "tremendous boost" to Iran's pursuit of nuclear weapons.
Centrifuges can be used to enrich uranium, or spin it at supersonic speeds to produce a concentrated material used to make nuclear weapons.
Satellite file image of Iran's
nuclear enrichment facility Natanz
When IAEA inspectors discovered working centrifuges at Iran's Natanz plant in February, Iran at first claimed to have built them alone.
But it later admitted they included second-hand components from another country, when inspectors detected traces of highly enriched uranium on the machines, which Iran insists it has never made.
Inspectors studying the machines also found that "the design is one of several known to have been stolen in the 1970s by Khan, who later become known as the father of the Pakistani bomb," the Post said.
The centrifuge blueprints included design modifications similar to ones made by Pakistan, and the uranium traces were consistent with material produced in Pakistan, the daily said.
All three of the scientists questioned - Faruq Muhammad, Yasin Chohan and Said Ahmad - were close aides to Khan, who retired in 2001.
Muhammad was in charge of dealing with foreign suppliers at his laboratory.
Pakistani media reports said Muhammad and Chohan were taken from their homes earlier this month, though Pakistani officials denied they had been arrested or detained. Chohan has since returned home but Muhammad is still being questioned.
Pakistan has strongly denied sharing nuclear technology with any other country
Khan himself is the main focus of the investigation, but the government of Pakistani President Pervez Musharraf has been reluctant to challenge him because of his status as a national hero, the Times said.
Pakistan, which declared its nuclear capability in May 1998 with a series of underground nuclear tests in response to similar detonations by rival India, has strongly denied sharing nuclear technology with any other country.