ABC News in the United States on Friday quoted intelligence sources as saying that senior al-Qaida operative Haitham al-Yemeni was killed by a missile fired from an unmanned CIA Predator aircraft.
The CIA has declined to comment on the report.
But Pakistan's Information Minister Sheikh Rashid Ahmed told Aljazeera that no such incident took place on the Pakistan-Afghanistan border.
"I have heard some news agencies reporting that Haitham al-Yemeni has been killed in Pakistan's border areas. However, as an official Pakistani spokesman, I deny this.
"No such thing has happened on Pakistani soil. What matters to Pakistan is that no one has been killed here, even if something has happened in Kabul or somewhere else."
Also on Saturday, a spokeswoman for the US military in Afghanistan, Lieutenant Cindy Moore, said forces from the US-led coalition in Afghanistan were not involved in such an incident, but she could not say whether it had taken place.
Pakistan which became an important ally of the United States in its war on terror after the 11 September 2001 attacks in America, earlier this month arrested Abu Faraj al-Libbi, reputed to be al-Qaida's number three leader.
ABC News reported that with the capture of al-Libbi, officials decided to strike at al-Yemeni rather than risk him going into hiding.