At least three people were killed and several more wounded as Iraqi troops stormed a prominent Sunni Muslim mosque in Baghdad Friday, with U.S. soldiers serving as backup.

There were conflicting reports on how many dead and wounded were left after the raid. The Associated Press said three were killed and five were wounded, while Reuters was reporting various casualty counts throughout the day.

Meanwhile, Iraqi forces continued the fight for Mosul (search), conducting several raids overnight in operations that left at least 15 insurgents dead.

At least 13 other insurgents were captured in Mosul, authorities said.

The Iraqi forces opened fire in the Abu Hanifa mosque (search) in Baghdad, long associated with anti-American activity, after Friday prayers, according to witnesses. Reuters reported that hundreds were in the mosque when the troops came through, and many began throwing shoes at the soldiers.

About 40 people were arrested during the operation in the capital city's northwestern Azamiyah neighborhood, said the witnesses, who were members of the congregation.

The raid at the mosque was apparently part of a crackdown on Sunni militant clerics launched in parallel with military operations against the Sunni insurgent stronghold of Fallujah (search).

Some witnesses told Reuters that the leader of the mosque was among those detained, but those reports could not be confirmed.

On Thursday, the Iraqi government warned that Islamic clerics who incited violence would be considered as "participating in terrorism." A number of them already had been arrested, including several members of the Sunni clerical Association of Muslim Scholars, which spoke out against the U.S.-led offensive in Fallujah.

"The government is determined to pursue those who incite acts of violence. A number of mosques' clerics who have publicly called for taking the path of violence have been arrested and will be legally tried," said Prime Minister Ayad Allawi's (search) spokesman, Thair al-Naqeeb.

U.S. troops also raided a Sunni mosque in Qaim, near the Syrian border, a cleric said, calling it retaliation for opposing the Fallujah offensive.

Imam Maudafar Abdul Wahab said his mosque was gathering food and supplies to send to Fallujah, and U.S. troops took about $2,000 meant for repair of his mosque.

Elsewhere in Baghdad, a homicide car bomber rammed into a police patrol setting up a checkpoint, killing one policeman and injuring as many as 10 other people, including other policemen, authorities said.

At the Abu Hanifa mosque, U.S. troops were seen securing the outer perimeter and sealing it off. Some American soldiers also were seen inside the compound.

Witnesses heard explosions coming from inside the mosque, apparently from stun grenades. Inside the office of the imam, books, including a Quran and a computer were found scattered on the floor, and the furniture was turned upside down.

At least 10 U.S. armored vehicles were parked at the mosque, along with two vehicles carrying about 40 Iraqi National Guards, witnesses said.

Abu Hanifa mosque has long been associated with anti-American agitation and support for the former regime. Saddam Hussein (search) was seen in the area as the city fell to American forces in April 2003. And U.S. Marines battled Saddam loyalists around the mosque on April 10, 2003, the day after the ousted ruler's statue was hauled down in Firdous Square.

Battle for Mosul

In the western part of the northern city of Mosul, Iraqi National Guard (search) members and a special police force made several raids Thursday night, killing 15 insurgents and capturing 10 others, Deputy Gov. Khasro Gouran said.

Three policemen also were killed Thursday when masked gunmen set up a checkpoint in eastern Mosul and shot them when they displayed identification, Gouran said.

A car bomb attack on a U.S. patrol in the northeastern Sukar neighborhood of Mosul injured one U.S. soldier, the military said.

The raid on the al-Zaharawi hospital in Mosul — Iraq's third-largest city — was conducted by Iraqi commandos with the Ministry of the Interior's Special Police Force, backed by U.S. troops.

Forces cordoned it off after getting information that insurgents were treating their wounded there, said Lt. Col. Paul Hastings with Task Force Olympia.

U.S. forces from the 1st Battalion, 24th Infantry Regiment secured the area around the hospital, while Iraqi troops raided the building, detaining three suspected terrorists.

Pictures were taken in the morgue of 23 bodies believed to have been those of insurgents, Hastings said.

U.S. and Iraqi forces began a major military operation Tuesday to wrest control of Mosul after gunmen last week attacked police stations, bridges and political offices in apparent support of Fallujah guerrillas.

On Friday, three of the city's five bridges were reopened to traffic and most of the city remained calm, though U.S. forces came under some "indirect fire" that caused no injuries, Hastings said.

During a routine patrol, U.S. forces also found burned ballot materials inside a Mosul warehouse after a tip by an Iraqi security officer. Efforts are underway to replace the materials for the January elections.

Al-Zarqawi's HQ Possibly Found

Iraq is slated to hold national elections by Jan. 31 to elect a 275-member assembly in what is expected to be a major step toward building democracy.

In Fallujah, battles flared as troops hunted holdout insurgents, and one U.S. Marine and one Iraqi soldier were killed, U.S. officials said.

U.S. troops sweeping through the city west of Baghdad found what appeared to be a key command center of terror mastermind Abu Musab al-Zarqawi (search), along with a separate workshop where an SUV registered in Texas was being converted into a car bomb and a classroom containing flight plans and instructions on shooting down planes.

The vehicle was surrounded by several bags of sodium nitrate, which can be used to make explosives. The vehicle had no license plate, but 15 plates were inside. Several bodies were found nearby.

The U.S. troops came across a large house with a sign in Arabic that said "Al Qaeda Organization," according to footage from a TV crew embedded with the U.S. Army.

Inside the house, an imposing structure with concrete columns, U.S. soldiers found documents, old computers, notebooks, photographs and copies of the Quran. Several bodies also were found.

There also were two letters, one from al-Zarqawi giving instructions to two of his lieutenants. Another sought money and help from the terrorist leader.

"This is a significant find," Van Hipp, a former deputy assistant Army secretary told FOX News. "It shows why we went to Fallujah. This was their base of operations."

Iraqi authorities have acknowledged that al-Zarqawi and other insurgent leaders escaped the invasion of Fallujah, which was launched as part of a campaign to restore order for the elections.

"We feel right now that we have, as I mentioned, broken the back of the insurgency. We've taken away this safe haven," Lt. Gen. John Sattler, commander of the 1st Marine Expeditionary Force, said at a base outside Fallujah.

Iraq Elections on Track

Rep. Dan Burton, R-Ind., told FOX News Friday that the U.S.-led operation in Iraq was going in the right direction, even though al-Zarqawi wasn't caught in the Fallujah offensive.

"There's no question we're on the right track," Burton told FOX. "Obviously, we didn't get him but perhaps ... those computers will help us [in] catching him in the not-so-distant future."

Burton said 15 of the 18 provinces in the Sunni Triangle would be ready to hold elections if they were held now, though they're still slated for the end of January. The anti-insurgency operations have been waged to clear the way for the national elections to go ahead as planned.

"I do expect there will be problems in other areas, but I do expect elections do go forward," Burton told FOX. "We're getting the job done."

The U.S. casualty toll in the Fallujah offensive stood at 51 dead and about 425 wounded. An estimated 1,200 insurgents have been killed, with about 1,025 enemy fighters detained, the military says.

Al-Zarqawi's group, Al Qaeda in Iraq, is blamed for dozens of deadly car bombings and the beheadings of foreign hostages, including three Americans. Washington has offered $25 million for information leading to al-Zarqawi's capture.

The extremist Ansar al-Sunnah Army, in a statement found Thursday on the Internet, threatened to attack polling stations and assassinate candidates because democracy is an "infidel" institution.

Iraqi authorities, meanwhile, said they arrested 104 suspected insurgents in a raid in Baghdad, including nine who had fled Fallujah.

Insurgents, though, struck back elsewhere in volatile Sunni Muslim areas. In Haditha, northwest of Fallujah, militants blew up the mayor's office and the police command center. Leaflets distributed by insurgents warned anyone who "wears a police uniform or reports to a police station will be killed."

Iraqi Forces Trained

Even as the fighting in Fallujah started to die down, training of Iraqi security forces was stepped up.

Senior U.S. commanders said the street-to-street, building-to-building fighting in Fallujah gave at least six battalions of Iraqi intervention forces "invaluable" combat training.

But they added that U.S. forces would have to shadow Iraqi troops inside Fallujah for a few more weeks in order to effectively respond to flare-ups.

While there were encouraging signs for the new Iraqi army and the national guard, the status of Iraqi police units was much more dismal.

In recent insurgent attacks in Mosul and other cities, the Iraqi police force essentially disintegrated, providing almost no defense.

Senior commanders said the Islamic extremists and former regime fighters were intimidating police officers, threatening their families, or paying top dollar for them to turn the other way — methods that were standard operating procedures in the former regime of Saddam Hussein.

"There was a culture of corruption and there was a culture of intimidation and we shouldn't think that just because we've been here for a year and a half that it's going to stop," Gen. John Abizaid told FOX News, who commands U.S. forces in the Middle East. "It will stop over time as people come to understand there is better way to live, and I'm confident that there are more good people in Iraq than bad people in Iraq."

The key, Abizaid said, was to find strong leadership for the Iraqi security forces, something U.S. commanders were pushing hard for — with just 10 weeks to go before Iraqi elections are scheduled to be held.

In other developments:

— U.S troops arrested a representative of Muqtada al-Sadr near the holy city of Karbala — the second arrest involving one of the radical Shiite cleric's aides in two days, al-Sadr's office said. On Thursday, another al-Sadr aide was arrested in Najaf for speaking out against the U.S.-led assault on Fallujah.

— U.S. troops were conducting an offensive in the northern Iraqi town of Hawija after a recent escalation of violence in the Sunni stronghold wounded three American soldiers and 10 Iraqi National Guards.

FOX News' Bret Baier, Ian McCaleb and The Associated Press contributed to this report.