The latest violence came as Iraqi and US troops fanned out across the capital as part of a long-awaited security plan to curb bloodshed that has killed tens of thousands across the country in the past year.
One of their targets on Thursday was the health ministry, where they arrested Hakim al-Zamili, the deputy health minister, the ministry's spokesman said.
"American forces accompanied by Iraqi forces broke into the ministry, forced the guards to lie on the floor and took Zamili," Qassem Allawi said.
US authorities have not said why Zamilia, a member of a group loyal to Moqtada al-Sadr, the Shia leader, was arrested.
Allawi said: "They [the US and Iraqi forces] have terrified all the [ministry] employees because they were breaking doors and smashing things. Some of the employees ran to the streets."
Nasar Al-Rubaee, head of Moqtada Al Sadr's block in the Iraqi parliament, told Al Jazeera the Us action ammounted to a "kidnapping". He said is was "unlawful and illegal becuase there is no warrant."
On Wednesday, the US military confirmed that its Baghdad security plan had got under way.
About 30 security stations manned by Iraqi police and army units and under 24-hour US troop surveillance are involved in the plan.
The security stations are intended to supplement Baghdad's existing 54 Iraqi police stations.
Ten of the new security stations are already in operation, major-general William Caldwell, a US military spokesman, said on Wednesday.
Caldwell, said: "Ten are up and running, and there's going to be at least double, if not triple, that number that will eventually be out there."
Baghdad's security plan aims to deploy up to 85,000 US and Iraqi troops on the streets.
|Al Jazeera showed exclusive footage |
of the downed military helicopter
US officials have also said a helicopter belonging to a private security firm was shot down last week near Baghdad, bringing the number of downed helicopters to six in three weeks.
The incident occurred on January 31, but was reported by US officials on Thursday, coming a day after a US Sea Knight helicopter crashed, possibly after it was hit by fire from the ground, killing seven people.
The New York Times, quoting US officials, reported the helicopter was shot down south of Baghdad after insurgents attacked it with heavy-calibre ground fire.
"It did not crash, it made a hard landing. They were able to get all crew and equipment out," the official said.
The US military has said it is "adjusting its tactics" in response to the helicopter crashes, raising concerns that militants have changed their tactics and are using more sophisticated weapons.