"There is no such collaboration," foreign ministry spokesman Masood Khan said, referring to an article in the New Yorker magazine that claimed Pakistani scientists were providing the US with information on Iranian nuclear sites.
"We do not have much information about Iran's nuclear programme so I think this report is far-fetched and it exaggerates facts which do not exist in the first place," Khan told a weekly press briefing in Islamabad.
"I do not think there is any substance in what has been reported. I think this is pure conjecture."
The New Yorker said Pakistan was helping the US in return for guarantees that it will not have to hand over disgraced nuclear scientist Abdul Qadeer Khan to international authorities for questioning.
Khan, the architect of Pakistan's nuclear programme, in February took responsibility for transfers of nuclear technology to Iran, Libya and North Korea. He was pardoned by President Pervez Musharraf.
The magazine said Pakistani scientists were giving information to be used by US commandos searching for underground nuclear installations in eastern Iran.