(Adds ministry comments, universities not closed)

By Aseel Kami

BAGHDAD, Nov 14 (Reuters) - Gunmen in Iraqi police uniforms rounded up as many as 100 men at a government building in central Baghdad on Tuesday, in what may be the biggest mass kidnap seen in a city becoming used to such violence.

It bore the hallmarks of sectarian militias operating under cover of the security forces, although senior officials and witnesses differed over how far minority Sunnis were the target.

Interior Ministry spokesman Brigadier Abdul Kareem Khalaf said security forces were hunting various districts of Baghdad for the kidnappers, who he described as "criminal groups". He said at least three of those taken had later been released.

Iraqiya state television reported the interior ministry had ordered the arrest of the police commander and another senior officer in Karrada, the district where the kidnapping happened.

Hours later a car bomb killed at least 10 people at a crowded central market, and wounded 25, police said.

The kidnap attack on the Higher Education Ministry building was a new blow to Iraq's battered universities, where dozens of professors have been killed since the U.S. invasion.

Higher Education Miniser Abd Dhiab said staff might now choose to stay away from work, though he later denied that he was calling for a shutdown.

A witness who works in the building but had stepped out when the gunmen arrived said he returned to see police standing idly by as the kidnappers checked identity cards, apparently sorting Sunnis from Shi'ites and then drove off with Sunni men.

However senior officials, often keen to play down sectarian tension, said men from both Muslim sects were taken. Shi'ites were among distraught relatives seeking information on missing family members after the raid in the central Karrada district.

Another witness saw men struggle before being bundled away.

"It's a terrorist act. They kidnapped more than 100 employees and visitors," said Dhiab, a member of the main Sunni Arab political bloc.

He told Reuters 13 of those initially taken had been released, and some of them said the gunmen headed eastwards, in the direction of the Shi'ite militia stronghold of Sadr City.

Both Sunni insurgents and Shi'ite militias have been blamed for mass kidnappings in the past and on occasions gunmen have released some of those initially seized, based on their sect.

Elsewhere, Iraqi officials said U.S. raids in a Shi'ite district of Baghdad and in the Sunni insurgent stronghold of Ramadi killed six and at least 30 people respectively overnight. The U.S. military had no immediate comment.

PRESSURE

Unrelenting violence has added to the pressure on Prime Minister Nuri al-Maliki to crack down on militias, some of which are linked to his Shi'ite political allies.

U.S. President George W. Bush has also said he is open to "fresh perspectives" to stem the violence in Iraq after his Republicans suffered a "thumping" at midterm elections last week, partly due to dismay over the war.

Numerous mass kidnappings have been blamed on gunmen operating either within the security forces or with their help.

Saddam Hussein's once dominant Sunni minority and U.S. officials have focused suspicion on militias from the Shi'ite Muslim parties, who control the Interior Ministry. The ministry has repeatedly denied charges of links to Shi'ite militias.

Washington, under mounting domestic political pressure to start pulling its 150,000 troops out of Iraq, has placed a heavy emphasis on recruiting and training Iraqi security forces, but their competence and sectarian loyalties remain in doubt.

Minister Dhiab said both Sunnis and Shi'ites were seized in the raid, which cleared the four-storey building of all staff and visitors, from directors to guards and teaboys. He said it was a well-planned operation that took no more than 15 minutes.

Women were separated from the men and locked in a room after having their mobile phones confiscated by the gunmen.

One witness, who is well known to a Reuters employee but did not want to be identified for fear of retribution, said when he returned to the building from an errand he saw around 40 pickup vehicles of the type used by police commandos.

"They were checking identity cards in the car park. They picked only the Sunni employees. They even took the man who was just delivering tea," said the witness, who is a Sunni Arab. "At the same time I saw two police patrols watching, doing nothing."

Dhiab said the attack, which follows the assassination of several leading academics in recent months, called into question the future of the university system in Iraq. "How can I ask our employees to go to their offices?" he said in parliament.

Academics contacted by Reuters said they had received no instructions as yet but said the recent killings and kidnaps had already led to teachers staying away and discussions on whether keeping their institutions open was still a viable option. (Additional reporting by Ahmed Rasheed, Ibon Villelabeitia, Mussab Al-Kharailla, Khaled al-Ramahi and Alastair Macdonald)

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