Iraq's deputy health minister was arrested by US and Iraqi soldiers for his alleged role in the country's sectarian conflict today in the first major act of the much-vaunted security plan to bring order to Baghdad.

Hakim al-Zamili, a member of the radical Shia movement loyal to the cleric Moqtada al-Sadr, surrendered to American soldiers when they raided his first floor office in the Health Ministry this morning, witnesses said. A US military statement later said the minister had allowed his department to assist in "sectarian kidnapping and murder".

His detention comes a day after the chief US military spokesman in Baghdad, Major General William Caldwell, announced that the joint US and Iraqi operation to swamp Baghdad with soldiers and crack down on the endemic violence in the city had begun.

It also follows months of allegations that the Health Ministry, its facilities and hospitals, have become de facto outposts for Shia militias, above all members of the al-Mahdi Army, the largest and most-feared Shia armed group in the country. Sunni MPs have complained of dozens of cases of Sunni Muslims being refused treatment in hospital and even being shot in their beds.

Iraq's Health Minister, Ali al-Shemari, another Shia Muslim who also has been linked to Moqtada al-Sadr, condemned the arrest. "This is a violation of Iraq’s sovereignty," he said. "They should have a court order to carry out a raid like this."

A US military statement refused to name Mr al-Zamili but said that the detained official was "suspected of funding rogue JAM (al-Mahdi Army) through large-scale employment of militia members".

“These militia members are reported to target Iraqi civilians using MoH (Health Ministry) facilities and services for sectarian kidnapping and murder. The suspect’s corruption is believed to have funnelled millions of US dollars into rogue JAM.”

In particular, Mr al-Zamili has been implicated in the disappearance of Dr Ali al-Mahdawi, a Sunni official who ran the Diyala Health Directorate. Dr al-Mahdawi and members of his staff have not been seen since they arrived at the Health Ministry headquarters in Baghdad for an interview last June.

Mr al-Zamili's Shia connections have made him a target of Sunni extremists. Last November, he survived an assassination attempt when gunmen attacked his convoy, killing two bodyguards. The day before, another deputy health minister, Ammar al-Assafar, had been kidnapped. Two days later, Sunni gunmen surrounded the Health Ministry, only withdrawing when US troops and aircraft and intervened.

A Health Ministry spokesman said Iraqi and American soldiers stormed the department's headquarters at the beginning of the working day. One of Mr al-Zamili’s bodyguards said he heard gunshots, then the US troops asked him to step aside and approached the deputy health minister, who introduced himself by name and title.

The minister was told he was on a list of wanted officials, the American soldiers said, according to the bodyguard, before being led away.

US forces and the Iraqi military have made strenuous, visible efforts in recent weeks to curb the influence of the al-Mahdi Army and officials perceived to be too close to Moqtada al-Sadr, claiming to have detained more than 600 members of the cleric's movement.

Breaking the Shia grip on Iraqi government departments is a priority for the US plan to halt the country's slide into civil war, but it is proving a severe test for Nouri al-Maliki, Iraq's Shia Prime Minister, who relies on sectarian allies for his support.

In recent weeks he has been accused of leaving Baghdad's Shias open to attack from Sunni extremists because of the operations against Shia militias that, until now, have been able to provide protection. Last Saturday more than 130 people died when a massive truck bomb exploded at Sadriya market in a Shia neighbourhood.

Today a spokesman for Moqtada al-Sadr's faction said that the arrest of Mr al-Zamili marked a new level of interference among Shia officials. "Zamili is in the government. Maliki should not just keep watching. Maybe tomorrow they will arrest him too,” Abdel Mahdi al-Matiri told Reuters.

Elsewhere across Iraq, violence claimed the lives of at least 43 Iraqis while the US military announced that four soldiers had been killed in Anbar, the unsettled western province.

The US Embassy in Iraq said it was investigating reports that a US civilian helicopter had been shot down on January 31. If the aircraft was brought down by ground fire, it would bring to six the number of American helicopters destroyed by insurgents in the last two weeks, a trend that has prompted a review of flights in the capital.

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