The source was reacting to Arab media reports that secret Iranian-Egyptian talks are underway concerning the suspects.
"There are absolutely no contacts between Egypt and Iran about the possible extradition of any Egyptians Iran may be holding," the source said.
Iran has said it is holding an unspecified number of al-Qaida suspects and is in discussions with unnamed "friendly countries" about turning them over.
Western governments believe Tehran is holding some of the world's most wanted al-Qaida suspects.
Many of Usama bin Ladin's top advisers are Egyptians including his deputy Ayman al-Zawahri and Saif al-Adel, the group's suspected military chief.
Both men have been linked to Egypt's Islamic Jihad group.
Iran however has denied holding al-Zawahri but has not commented on Adel.
A London-based Egyptian Islamist Yasir el-Serri has downplayed the possibility that Iran was holding high-level al-Qaida officials.
"Zawahri would not take the risk and enter Iran," he said.
Serri claimed Iran had rejected Zawahri's efforts to enter the country in 1996 and other high-ranking al-Qaida officials would have left Iran after earlier extraditions.
"Iran has extradited up to a dozen low-level members of the group to Egypt over the past year," Serri, who has been convicted in his home country for militant activities said.
Egypt and Iran do not have full diplomatic ties but maintain representative offices in each other's capital.
Relations were broken off in the wake of the 1979 Iranian revolution whose leaders denounced Egypt for its peace moves with Israel.