Saedi was "captured a few days ago along with a group of his loyalists after an operation was carried out by Iraqi security forces supported by US forces", national security advisor Muwaffaq al-Rubaie said.
Saedi was the number two leader after Abu Ayyub al-Masri of the al-Qaeda Islamist network in Iraq.
Masri was appointed as the group's Iraq commander after the June 7 slaying of Abu Musab al-Zarqawi in a US air strike near the restive provincial capital of Baquba, north of Baghdad.
"Saedi was arrested north of Baquba not far from the location where Zarqawi was killed," Mr Rubaie said.
"During the raid, Saedi took shelter in a residential building, but he was arrested without any harm to civilians," he said.
Suspects captured
Saedi is accused of ordering the February 22 bomb attack that demolished a Shiite shrine in the town of Samarra, north of the capital.
During the raid to capture Saedi, 11 other senior al-Qaeda operatives and nine other suspects were also detained.
Saedi's arrest dealt a severe "blow to al-Qaeda in Iraq, especially their activities aimed at inciting sectarian conflicts", according to Iraqi officials.
Saedi supervised terrorist groups that kidnapped people for ransom and also operated several death squads.
"His terrorist attacks using mortars and roadside bombs killed many troops and civilians," Mr Rubaie said.
In June Rubaie announced the capture of a Tunisian al-Qaeda militant 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, Mr Rubaie said that Badri had taken orders from Saedi to bomb the shrine. Badri remains at large.
Flag row
Meanwhile, a new row broke out as Prime Minister Nuri al-Maliki set himself on a collision course with Kurdish leaders by ordering public buildings across Iraq to fly the national flag.
"The present Iraqi flag should be hoisted on every inch of Iraqi soil until the parliament takes a decision about it," Mr Maliki said in a statement issued by his office.
Massud Barzani, president of the autonomous Kurdish regional government, last week raised separatist tensions after he banned the Iraqi flag from government offices in the region, leaving the Kurdish colours to fly alone.
Mr Barzani insisted he had consulted Maliki, a Shiite Arab, and President Jalal Talabani, a fellow Kurd, before ordering the national flag taken down.
"The decision came after consultation with both President Talabani and the Iraqi prime minister. I haven't made the decision by myself," he said.
In a scathing attack on Iraqi Arab politicians, Mr Barzani said: "Those who condemn it are chauvinists escaping from internal problems.
"They are losers. They are not rulers or statesmen. They can't run their own region and they want to make Kurdistan just like their region.
"The time of threatening is over. No one has the right to force his will on the Kurdish people."
Iraq's Kurdish minority associates Iraq's red, white and black banner with Saddam Hussein’s hated Baath party, although it has been retained as the national flag by the post-Saddam government in Baghdad.
Iraq PM to visit Iran
Meanwhile Iraqi Prime Minister Nuri al-Maliki is due to make his first visit to Iran as head of the Baghdad government next week.
Iranian state television reported that his deputy Barham Saleh would be visiting Tehran tomorrow in order to prepare the ground for the visit by Mr Maliki.
The Shiite prime minister lived in Iran in the 1980s in order to escape persecution of his Dawa party by Saddam Hussein.
The two countries waged a war between 1980 and 1988 in which around one million people died but ties have warmed considerably since the fall of Saddam, with the Islamic republic becoming a close ally of the Shiite-led Iraqi government.