Hamed Jumaa al-Saedi, Al Qaeda's No. 2, has been arrested in Iraq, National Security Adviser Muwaffaq al-Rubaie said on Sunday.
Saedi was earlier detained in June, and had ordered the blowing up of a revered Shia shrine in Samarra in February.
The incident had triggered nationwide Shia-Sunni sectarian killings.
Saedi was arrested in a joint Iraq-US raid north of Baquba and 11 top Al-Qaeda operatives and nine lesser suspects were also detained, Rubaie said.