Pakistan has denied that President Pervez Musharraf told a German magazine that Iran was "very keen" to have a nuclear bomb.
President Musharraf said a US strike on Iran would be "a disaster"
Iran demanded an urgent clarification after the comments were carried in Der Spiegel magazine on Saturday.
Pakistan's foreign office spokesman, Jalil Abbas Jilani, said the president had been misquoted.
Iran, under an international nuclear investigation for two years, says its industry is for peaceful purposes.
In the magazine article, President Musharraf said he did not know how to stop Iran from developing a military nuclear programme.
Mr Jilani confirmed this, but the magazine also quoted President Musharraf as saying: "They are very keen to have the bomb."
Mr Jilani said the president had not made the remark.
But Der Spiegel said it was standing by its interview with the president.
The interview had brought a quick reaction from Iran.
Iranian foreign ministry spokesman, Hamid Reza Asefi, told the AFP news agency on Sunday he thought it "very unlikely that [President] Musharraf said such a thing, because he knows better".
He added: "We hope that the Pakistanis explain that this report was distorted."
Mr Asefi added: "It is not the business of other countries to comment in this regard. It is up to us to say what we are seeking and not seeking. We are insisting we are not seeking such weapons."
Pakistan has been closely linked with Iran's nuclear industry since the revelation that disgraced Pakistani scientist Abdul Qadeer Khan illegally transferred nuclear technology to Iran and other countries.
Islamabad recently sent parts of its nuclear centrifuges to the UN's International Atomic Energy Agency (IAEA) in Vienna as part of the two-year investigation into whether Iran has been trying to building an atomic bomb.
The IAEA wants to check whether traces of enriched uranium found at an Iranian nuclear site in 2003 were illegally supplied by Dr Khan.
The IAEA investigation has found no proof that Iran plans to build nuclear weapons but has also been unable to confirm that the programme is entirely peaceful.
The US has accused Iran, a state already rich in gas and oil, of pursuing atomic energy as a screen to develop weapons.
In the Der Spiegel article, President Musharraf was also quoted as saying that a US attack to stop Iran developing nuclear arms would be "a disaster".
"That would provoke a rebellion in the Muslim world," he was quoted as saying. "Why open up new fronts?"