Saif al-Adel, identified as a senior al-Qaeda leader, has been arrested at Cairo airport in Egypt on Wednesday, security officials said.
Al-Adel was widely reported to have assumed leadership role in the militant network after the death of the Osama bin Laden.
On Wednesday, he arrived in the Egyptian capital from Pakistan on a flight, which had stopped in Dubai, an airport official told the AFP news agency.
However, the officials did not reveal why al-Adel, who is on the FBI's most wanted list with a $5-million reward on his head, flew to Cairo.
According to the FBI Web site, the Egyptian is wanted in connection with the August 7, 1998, bombings of the United States Embassies in Dar es Salaam, Tanzania, and Nairobi, Kenya.
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The former Egyptian army officer, whose real name is Muhammad Ibrahim Makkawi, was once bin-Laden's security chief and managed the terror outfit's military operations.
The FBI also said on its website that, al-Adel is thought to be affiliated with the Egyptian Islamic Jihad (EIJ), and is believed to be a high-ranking member of the al-Qaeda organisation.
However, Aljazeera reported, quoting an airport source, that al-Adel claimed he had left al-Qaeda long time ago.
According to security officials, al-Adel was taken into custody by the National Security apparatus.