Interior Minister Habib al-Adli did not disclose where Mustafa Hamza, leader of the al-Gamaa al-Islamiya group, had been extradited from, but last month an Egyptian security official and an activist of the group said Hamza had been turned over by Iran.
But Iran has denied holding Hamza or returning him to Egyptian custody.
"We have received Mustafa Hamza and he will face a retrial as soon as possible," al-Adli said in Tunisia, the Middle East News Agency reported on Saturday.
Egyptian authorities first arrested Hamza in 1981. He served three years in prison in the case of the 1981 assassination of former Egyptian president Anwar Sadat. On his release, he went to Afghanistan.
Egyptian courts since sentenced Hamza to three death sentences on charges of involvement in operations in Afghanistan in 1992 and in Sudan in 1995 and also for the attempt on the life of Mubarak during a 1995 visit to Addis Ababa, Ethiopia.
"He is from the very dangerous elements and getting to him is a success"
Egyptian Interior Minister
"He is from the very dangerous elements and getting to him is a success for the security apparatus and good bilateral relations between Egypt and other countries," he said.
It had been widely believed that Hamza, 48, had been under house arrest in Iran since October 2003.
Sinai bombing suspects
In 1996, Hamza's name was on a list of the 14 "most dangerous, wanted Egyptians abroad". He was allegedly in charge of his group's military wing, which carried out anti-government attacks during the 1990s aimed at toppling Mubarak's government and replacing it with Islamic rule.
However, when al-Gamaa al-Islamiya - or the Islamic Group - renounced violence in 1997, Hamza supported the decision and agreed two years later to halt all attacks inside and outside Egypt.
Meanwhile, al-Adli said police were closing in on two key suspects in the October Sinai Peninsula bombings that killed 34 people, including Israelis, Egyptians, Italians and Russians.
Nine people, including a Palestinian, have already been charged with near simultaneous bombings on the beachside Ras Shitan camping area and the Taba Hilton resort on the Egyptian-Israeli border.
"We are close to reaching the remaining suspects at large in the Taba explosions, plus a third element who helped them hide," al-Adli said.