The clash occurred near Balad, a major U.S. base about 50 miles north of the capital, Brig. Gen Abdul-Karim Khalaf said.
Khalaf said al Qaeda in Iraq leader Abu Ayyub al-Masri was wounded and his aide, identified as Abu Abdullah al-Majemaai, was killed.
Khalaf declined to say how Iraqi forces knew al-Masri had been injured, and there was no report on the incident from U.S. authorities. Deputy Interior Minister Maj. Gen. Hussein Ali Kamal said he had no information about such a clash or that al-Masri had been involved.
Al-Masri took over the leadership of al Qaeda in Iraq after its charismatic leader, Abu Musab al-Zarqawi, was killed in a U.S. air strike last June in Diyala province northeast of Baghdad.
Meanwhile U.S. and Iraqi forces pushed deeper into Sunni militant strongholds in Baghdad — where cars rigged with explosives greeted their advance — while British-led teams in southern Iraq used shipping containers to block suspected weapon smuggling routes from Iran.
The series of car bomb blasts, which killed at least seven civilians, touched all corners of Baghdad. But they did little to disrupt a wide-ranging security sweep seeking to weaken militia groups' ability to fight U.S.-allied forces — and each other.
The attacks, however, pointed to the critical struggle to gain the upper hand on Baghdad's streets. The Pentagon hopes its current campaign of arrests and arms seizures will convince average Iraqis that militiamen are losing ground.
It will take a lot of convincing.
Iraqis, such as Sunnis living on Haifa Street in central Baghdad, still live in mortal fear, reports CBS News chief foreign correspondent Lara Logan.
"Right now it is very difficult with the enemy that is around here in this area — it is a real hostile area," says Lt. Juan Cantu, whose Crazyhorse Troop is guarding Haifa Street. "These people are scared just to go outside their front door."
In other developments:
Most of the latest resistance has come from Sunni factions, which perceive their Saddam Hussein-era influence slipping away as the majority Shiites extend their political muscle and bolster ties to Iran.
In Baghdad's Dora neighborhood — a longtime Sunni militant hotbed — two parked cars wired with explosives were triggered as a joint U.S.-Iraqi patrol rolled pass. The convoy was unharmed, but the blast killed at least four civilians and injured 15.