US-backed Iraqi forces stormed the Health Ministry and arrested the No. 2 official, accusing him of diverting millions of dollars to the biggest Shiite militia and allowing death squads to use ambulances and government hospitals to carry out kidnappings and killings.
Shiite politicians allied with anti-US cleric Moqtada al-Sadr denounced the arrest of Deputy Health Minister Hakim al-Zamili on Thursday as a violation of Iraqi sovereignty and demanded that the prime minister intervene.
But Prime Minister Nouri al-Maliki and his senior advisers remained silent. Al-Maliki, a Shiite, is under strong US 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.
The arrest took place at 9am, 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 US soldiers accompanying the force asked everyone to step aside and approached the deputy minister, who introduced himself. A US soldier handcuffed al-Zamili and led him away, the guard said on condition of anonymity because he feared reprisal.
A US military statement did not mention al-Zamili by name but said Iraqi special troops had 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."
US military spokesman Lieutenant Colonel 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."
US 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 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.
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.
US 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 pressure, al-Maliki's aides said.
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 any time soon.
At least 104 people were killed or found dead on 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 80km 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, 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.
In Anbar Province west of Baghdad, a US airstrike 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, leaving 45 people dead, including women, children and old people.
Also on Thursday, the US announced that four US Marines were killed the day before in fighting in Anbar, an insurgent stronghold.
At least 3,114 members of the US military have died since the Iraq war started in March 2003.
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