The man was identified as Abu al-Faruq, a Syrian who is said to have financed and coordinated groups working for Abu Musab al-Zarqawi in Ramadi, where fighting against the US-led invasion has been strongest.
The information came from an Interior Ministry officer who spoke on condition of anonymity because he was not authorised to address the media.
Acting on a tip from residents, members of the ministry's Wolf Brigade captured al-Faruq with five other people near Bakr, about 161km (100 miles) west of Baghdad, the officer said.
The Defence Ministry said Iraqi security forces had killed 35 fighters and arrested 487 in raids across the country since the bombing last Wednesday of the Samarra shrine.
Fighting escalated after the bomb attack on 22 February, with some arguing the country was on the verge of civil war.
Shrine bombing aftermath
On Tuesday, Zalmay Khalilzad, the US ambassador to Iraq, said this risk was now over, although sporadic fighting persisted. Aljazeera reported that tanks were still patrolling the streets of Baghdad.
On Monday 36 people died across Iraq, mainly in battles between Iraqi commandos and fighters southeast of the capital.
Iraqi special police commandoes
also called the Wolf Brigades
But Baghdadis returned to their jobs after three days of a government-imposed curfew.
Tea vendor Abbas Kudir said: "We were at home for three days doing nothing.
"We are of limited income. We earn money when people can come and buy tea normally. We hope the government will pay attention to our difficulties."
Sunni Arab leaders have said they are prepared to end their boycott of the talks on a new government if the Shia return mosques seized in reprisal attacks against Sunnis and meet other unspecified demands.
"That crisis is over," Khalilzad said.
"I think the country came to the brink of a civil war, but the Iraqis decided that they didn't want to go down that path, and came together," the ambassador told CNN.
Also on Monday, Iraqi Interior Ministry officials said they believed Jill Carroll, the American journalist kidnapped on 7 January was still alive.
Jill Carroll was working for the
Christian Science Monitor
A senior ministry official refused to say why they did not believe Carroll's captors carried out their threat to kill the 28-year-old freelancer for the Christian Science Monitor.
The speed with which attacks spread from Samarra to Baghdad and southern Iraq has raised concerns about the ability of Iraq's understaffed and ill-equipped security forces to handle the crisis.
Sunni leaders accused the Shia-dominated police and army of standing by as Shia militiamen sprayed their mosques with machine-gun fire and took over some of them.
The Washington Post reported on Tuesday that more than 1300 Iraqis had been killed in the violence following the Samarra shrine attack, citing Baghdad's main mortuary.
The US releases an image of a
weapons cache found in al-Anbar
The newspaper said the statistics department of the Iraqi police put the nationwide toll at 1020 since Wednesday, but added the paperwork on deaths was sometimes delayed.
The Defence Ministry said a curfew in Baghdad and three surrounding provinces curtailed the violence.
The violence threatened US plans of a broad-based government capable of appealing to Sunni Arabs.
Adnan al-Dulaimi, whose Iraqi Accordance Front spearheaded the Sunni walkout from the talks, said the Sunnis were "intent on participating" in a new government but were holding out for some conditions to be met.
An Iraqi soldier on guard at a
Shia mausoleum in Baghdad
The US State Department praised the Sunni leadership as "looking to get back into the game, full strength" and brushed aside the additional demands.
Adam Ereli, the deputy spokesman in Washington, said: "The conditions are less important than the fact that there are good-faith discussions going on about resuming full-bore talks on a national unity government."
A spokesman identified the Iraqis captured and killed since Wednesday as linked to various groups, including al-Qaida in Iraq, but could not confirm whether any of them took part in the Samarra bombing.
US helicopters fired on three houses west of Samarra and arrested 10 people, Iraqi police said. It was unclear if the raid was linked to the shrine bombing. The US military did not comment.
Interior Ministry commandos fought a three-hour battle with fighters near Nahrawan, southeast of Baghdad, after about 15 Shia families were driven from their homes in the village of Saidat, police said.
At least eight commandos and five fighters were killed. Six commandos and four civilians were injured, police said.
The body of an official with Iraq's largest Sunni Muslim political group was delivered to the Health Ministry mortuary on Monday with signs of torture, his party said.
Waad Jasim al-Ani, a member of the Iraqi Islamic party, was seized from his home on Saturday by an unspecified security agency, the party said.
Sunni leaders accuse Iraq's Shia-led Interior Ministry of running death squads that target them - a charge denied by the ministry.
The US military said an American soldier had died from non-combat related injuries suffered on Friday north of Baghdad. Three soldiers were killed on Sunday in combat operations in the capital.
The US military toll has reached
2291 according to AP
Their deaths brought to at least 2291 the number of US military personnel who have died since the beginning of the Iraq war in March 2003, according to an Associated Press count. The figure includes seven military civilians.