Shiite politicians allied with anti-American cleric Muqtada al-Sadr denounced the arrest of Deputy Health Minister Hakim al-Zamili as a violation of Iraqi sovereignty and demanded that the prime minister intervene to win his release.
CBS News chief foreign correspondent Lara Logan spoke to Ali-al-Shammari, the outraged Iraqi Health Minister, who protested the innocence of his deputy.
"I will not accept that he will work with me and at the same time he is kidnapping or killing other people," he said.
But Prime Minister Nouri al-Maliki and his senior advisers remained silent. Al-Maliki, a Shiite, is under strong U.S. pressure to crack down on Shiite militias and has pledged not to interfere in the security operation to rid Baghdad's streets of gunmen from both Islamic sects.
Logan reports that al-Zamili is suspected of allowing al-Sadr loyalists easy access to Baghdad's hospitals, where the militants would often kill doctors, nurses, and family members who came to visit loved ones injured in the daily attacks - or to collect their bodies.
The arrest took place at 9 a.m., an hour after Iraqi government offices generally open. Iraqi troops pushed through the iron gates of the Health Ministry building in northern Baghdad, ordered people to drop to the ground and rushed to al-Zamili's ground-floor office, witnesses said.
One of al-Zamili's bodyguards said American soldiers accompanying the force asked everyone to step aside and approached the deputy minister, who introduced himself. A U.S. soldier handcuffed al-Zamili and led him away, the guard said on condition of anonymity because he feared reprisal.
AP Television News footage of al-Zamili's office showed overturned chairs and smashed computers along with scattered files and telephones on the floor. Dusty, white boot prints marked the door, apparently because the troops had kicked it in.
This arrest is seen in Iraq as a test of wills that will reveal how far the Iraqi Prime Minister is prepared to go in alienating his allies and supporting the latest U.S. effort to secure Baghdad, Logan reports.
Meanwhile, in Anbar province west of Baghdad, a U.S. air strike killed 13 insurgents in a raid on two safe houses where intelligence showed foreign fighters were assembled near Amiriyah, the military said. Five militants were detained and a weapons cache was found in an initial raid on a target near the safe houses.
Police and hospital officials in the area offered a conflicting account, saying the airstrike hit the village of Zaidan south of Abu Ghraib and flattened four houses, killing 45 people, including women, children and old people.
In other developments:
A U.S. military statement did not mention al-Zamili by name but said Iraqi special troops captured a "senior official" suspected of alleged corruption and links to al-Sadr's Mahdi Army militia. The Health Ministry is among six Cabinet posts controlled by al-Sadr, an ally of the prime minister.
The statement also alleged the senior official played a role in the deaths of several ministry officials, including the Sunni director of health in Diyala province. The director, Ali al-Mahdawi, vanished last June after coming to Baghdad for a meeting at the ministry.
According to the statement, the official was believed to have siphoned millions of dollars from the ministry to the Mahdi Army "to support sectarian attacks and violence targeting Iraqi citizens."
U.S. military spokesman Lt. Col. Christopher Garver said militiamen were also allowed to use government hospitals and clinics to gather information on Iraqis seeking treatment and "those Iraqis that were discovered to be Sunnis would later be targeted for attacks."
American officials had long complained that al-Sadr's followers were transforming hospitals into bases for the Mahdi militia and were diverting medicine from state clinics to health care facilities run by the cleric's movement.
The clinics helped al-Sadr build a powerful nationwide political movement modeled in part on the Shiite Hezbollah militia in Lebanon.
The arrest is likely to add new strains to al-Maliki's fragile coalition as it embarks on a high-risk campaign to curb violence in Baghdad. Shiite politicians persuaded al-Sadr to pull his militiamen back from the streets in the run-up to the security campaign.
But a series of bombings and suicide attacks on Shiite civilians in Baghdad and the southern city of Hillah has led many Shiites to complain that U.S. and Iraqi forces have not launched the security campaign fast enough to protect them against Sunni extremists.
Nasr al-Rubaie, leader of the Sadrist bloc in parliament, called al-Zamili's arrest a "kidnapping."
Health Minister Ali al-Shemari also denounced the raid.
"This is a violation of Iraq's sovereignty," he said. "They should have a court order to carry out a raid like this."
U.S. officials have insisted that al-Maliki rein in al-Sadr's forces, and the prime minister told the cleric last month that he could no longer provide him with political protection in the face of U.S. pressure, according to al-Maliki's aides.
Curbing the militias is considered key to halting the wave of Sunni-Shiite reprisal killings that surged after last year's bombing of a Shiite shrine in the mostly Sunni city of Samarra.
Despite recent efforts, the violence showed little signs of receding.
At least 104 people were killed or found dead Thursday in Iraq, including at least 10 Sunni men gunned down in the village of Rufayaat, just east of Balad. Balad is a majority Shiite town 50 miles northeast of the Iraqi capital, but it is surrounded by territory that is mainly populated by Sunnis.
In the day's deadliest attack, a parked car bomb exploded at a food market in the predominantly Shiite town of Aziziyah, 35 miles southeast of Baghdad, killing 20 people and wounding 45, police said.
Another parked car bomb tore through a minibus in the mainly Shiite Amin neighborhood of southeastern Baghdad, killing seven passengers and wounding 10, police said.
Also Thursday, the U.S. announced that four U.S. Marines were killed the day before in fighting in Anbar, an insurgent stronghold. At least 3,114 members of the U.S. military have died since the Iraq war started in March 2003, according to an AP count.
The U.S. Embassy in Baghdad, meanwhile, said U.S. officials were investigating a Jan. 31 incident involving a civilian helicopter after The New York Times reported that insurgents had brought the chopper down with ground fire during a flight between Hillah and Baghdad in support of State Department operations.
A Pentagon official, speaking on condition of anonymity because he was not authorized to disclose the information, said the helicopter belonged to the private security firm Blackwater USA. The official said the aircraft did not crash but rather landed and that the people aboard were safely evacuated.
If confirmed, it would be the second Blackwater helicopter and at least the sixth overall to go down in Iraq since Jan. 20, prompting the U.S. military to review flight operations. The most recent crash occurred Wednesday when a CH-46 Sea Knight went down northwest of Baghdad, killing seven people.