Alaa Makki, the head of the parliamentary education committee, said Shias and Sunnis had been abducted in raid and urged the government to rapidly respond to what he called a "national catastrophe".
"All interior ministry forces are on alert, searching for this group. We don't know if it's terrorists, militias or even government forces."
Brigadier Abdul Kareem Khalaf, interior ministry spokesman
Makki said the gunmen had a list of names of those to be taken and claimed to be on a mission from the government's anti-corruption body.
A female professor visiting at the time of the kidnappings said men and women had been forced into separate rooms, the men were then handcuffed and loaded onto about six pickup trucks.
The minister of higher education has stopped teaching in all of Baghdad's universities after the kidnapping.
"We have no other option than to halt the teaching of universities, at least in Baghdad, until we find out what happened," Abed Dhiab al-Ujaili said. "We are not ready to lose more professors."
Academics are increasingly being targeted in sectarian violence and thousands of professors and researchers have fled the country.
A university dean and a prominent Sunni geologist have been murdered in recent weeks taking the total to at least 155 education workers since the war began.
The security forces have been accused of taking part in or turning a blind eye to several previous mass kidnappings which are believed to have been carried out by sectarian militias.
|Mourners protested after six people |
were killed in a US airstrike
The Sunni minority have blamed many of the kidnappings on militias from the now dominant Shia parties, who control the interior ministry.
The Higher Education Ministry is headed by a member of the main Sunni Arab political bloc.
In Shula, a predominantly Shia area of western Baghdad, mourners protested about what Iraqi officials said was a US raid that killed six people.
The US military declined to confirm any operation in the neighbourhood.
Interior ministry sources said 13 people were also wounded after US troops called in an air strike when they came under fire from Mehdi Army militiamen loyal to cleric Moqtada al-Sadr.
Angry mourners chanted slogans criticising the US and supporting Sadr.