The foreign ministry reiterated that a "very small number" of Pakistani nuclear scientists were being investigated about the allegations.
But Pakistan had no information that the International Atomic Energy Agency (IAEA) wanted to question former premiers Benazir Bhutto and Nawaz Sharif, foreign office spokesman Masood Khan told reporters.
"We haven't heard anything about it because this is heresay," Khan said.
Local daily The News reported Sunday that the alleged transfer of nuclear secrets could have taken place before President Pervez Musharraf seized power in a military coup in October 1999.
Drawings on centrifuge technology, the main tool for enriching uranium, may have been supplied to Iran during Bhutto's 1988-90 rule, it said.
"The UN investigators at an appropriate stage intend to contact both prime ministers for ascertaining more facts on the case," the paper said, quoting highly placed sources in Vienna.
Sharif lives in exile in Saudi Arabia and Bhutto spends her time in London and Dubai.
Khan said no foreign agency was questioning the Pakistani scientists that were being "debriefed" about the allegations.
"The debriefing sessions are continuing, what we need here is patience," he said.
"These are internal briefings, they will take some time. I can't project a timeline."
Two nuclear scientists, Yasin Chohan and Farooq Mohammad, directors of the country's key facility of Kahuta Research Laboratory (KRL), were taken from their homes in early December for questioning.
Chohan has since returned home but Farooq is still being questioned.
Khan said the creator of Pakistan's nuclear bomb, Abdul Qadeer Khan, had also been questioned but denied his movements were restricted.
"When the government of Iran shared some information with us and subsequently the International Atomic Energy Agency asked for our cooperation, we started these debriefing sessions," he said.
Khan said "there is no witch-hunt" going on in the country and the scientists were cooperating. Pakistan was also cooperating fully with the IAEA.
"I think everybody concerned is cooperating with the concerned authorities," he said.
Islamabad went public as a nuclear power in May 1998 when it conducted underground nuclear tests.
But it has consistently denied reports that it has exported its nuclear know-how, a stance reiterated Monday by Khan, who said: "Pakistan has never proliferated and will never proliferate."
Musharraf has rejected the allegations as a smear campaign.