Mowaffak al-Rubaie, the Iraqi national security adviser, announced on Sunday that Hamed Juma Faris al-Saeedi, also known as Abu Humam or Abu Rana, had been arrested in an operation in mid-June.
Al-Rubaie said he was the deputy to Abu Ayyub al-Masri, who took over control of al-Qaeda's Iraq operations after US troops killed Abu Musab al-Zarqawi in June.
"During the raid, Saeedi took shelter in a residental building, but he was arrested without any harm to civilians," al-Rubaie added, without explaining why his arrest was not announced until nearly two months later.
Al-Saeedi is accused of ordering the February 22 bomb attack which demolished the Shia shrine in the town of Samarra, north of the capital.
Al-Rubaie said that during the raid to capture al-Saeedi, 11 other senior al-Qaeda operatives and nine lesser suspects were also detained.
"He was hiding in a building used by families, he wanted to use children and women as human shields as our forces attempted to capture him.
"We've got a very good capability that's growing within the Iraqi security forces that's able to take the challenge on"
Captain Frank Pascual, US military
"He was directly responsible for the criminal Haitham al-Badri, the mastermind and the bomber of the Samarra shrine.
"I can say that al-Qaeda in Iraq is severely wounded," al-Rubaie said.
A spokesman for the US military, Captain Frank Pascual, said the capture of al-Saeedi "demonstrates the growing capability of Iraqi security forces in fighting terror within their own borders, particularly al-Qaeda".
"We've got a very good capability that's growing within the Iraqi security forces that's able to take the challenge on, and which is able to capture, kill or drive them [al-Qaeda] away." he told Aljazeera.
The bombing of the Shia shrine in February inflamed tensions between Shia and Sunni Muslims and triggered reprisal attacks that still continue.
The Shia shrine in Samarra was
bombed on February 22
In June, al-Rubaie had announced the capture of a Tunisian al-Qaeda figure suspected of participating in the Samarra shrine bombing.
Abu Qudama al-Tunisi was accused of taking an active part in blowing up the mosque's golden dome on orders from an Iraqi militant, Haitham al-Badri.
On Sunday, al-Rubaie said that al-Badri had taken orders from al-Saeedi to bomb the shrine. Al-Badri still remains at large.
Al-Rubaie said the authorities had obtained information about al-Saeedi after the killing of Abu Musab al-Zarqawi in a US air strike north of Baghdad.
The information indicated that al-Saeedi had moved to northern Baghdad and had been operating outside Baquba, the same area where al-Zarqawi was killed.
Iraq and US officials have blamed al-Qaeda in Iraq for some of the worst attacks against civilians, which they say are part of a campaign to ignite a sectarian civil war between the majority Shia and minority Sunnis.