A report in the Daily Times made the claim Monday over Qadeer Khan, respected as a national hero and "father" of Pakistan's nuclear bomb for establishing a key nuclear facility near Islamabad, and said that he was being debriefed by officials.
The unspecified restrictions followed the detention and debriefing of two directors at Qadeer Khan's Kahuta Research Laboratories (KRL), the paper said.
But a foreign ministry spokesman Masood Khan said: "No restrictions have been imposed on him."
Qadeer Khan "is too eminent a scientist to undergo a normal debriefing session," the spokesman told AFP.
"However, some questions have been raised with him relating to the ongoing debriefing session," he added.
Local media reported this month that KRL directors Yasin Chohan and Farooq Mohammad were taken from their homes in early December for questioning.
Chohan has since returned home but Mohammad Farooq is still being questioned.
The Daily Times claimed that Iran had told the International Atomic Energy Agency (IAEA) that some top Pakistani nuclear scientists gave nuclear-related information to Tehran.
"The president was shattered when Iran named some Pakistani scientists," it said quoting an unidentified source, who said President Pervez Musharraf had ordered an investigation.
The foreign ministry spokesman said: "We have been fully cooperating with IAEA, the government of Pakistan has never authorized or initiated any transfers of sensitive nuclear technology."
The spokesman added that "a very small number" of individuals were under investigation.
"If they are found responsible at the end of debriefing sessions, we shall take action against such individuals if warranted and if they are found culpable under our laws. No body is above the law," he said.
"Pakistan takes its responsibility as a nuclear weapons state very seriously. Since a strict command and control system was established nothing of the sort has happened."
He also denied reports that US investigators were involved in questioning Pakistani scientists.
"These are purely in-house investigations. No foreigners or foreign agencies are associated with the debriefing sessions in sensitive organisations."
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.
However the New York Times reported Monday that information Iran turned over to the IAEA two months ago strengthened suspicions that Pakistan sold key nuclear secrets to Iran.
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