Security officials said the gunmen stormed the Al-Rawafed security company headquarters in eastern Baghdad and forcing the staff to leave the building at gunpoint.
Iraqi officials could not immediately say if the gunmen were from the interior ministry or if the employees had been kidnapped by insurgents disguised as police commandos.
Bodies found
The incident came less than 24 hours after police found the bodies of 18 men crammed into a minibus in a Sunni Arab district of west Baghdad. Some had been shot but most had been strangled.
The victims wore civilian clothes soaked in blood and the faces of several of them had turned blue. Two more bodies were discovered earlier in another part of Baghdad.
Fearing a fresh outbreak of sectarian violence between Sunnis and Shiites, interior ministry officials refused to say if the killings were sectarian in nature.
In other violence at least 11 Iraqis were killed and scores of others wounded in a series of rebel attacks. The dead included four Iraqi policemen and two soldiers.
The latest round of violence came as the US ambassador to Iraq, Zalmay Khalilzad, acknowledged that the US-led invasion had opened a "Pandora's box" of ethnic and sectarian tension in the region.
The bombing of a Shiite shrine in the northern town of Samarra on February 22 triggered the worst sectarian violence since the invasion and has left hundreds dead, mainly Sunnis.
Mr Khalilzad said Washington had little choice but to maintain a strong presence in Iraq or risk a regional conflict with Arabs siding with the Sunnis and Iran which backs the Shiites.
Parliament to open
Meanwhile Iraq's Shi'ite vice president has finally signed a presidential decree calling parliament into session.
The move has broken a political deadlock that had delayed the creation of a unity government in Iraq. US officials are hoping the formation of parliament will help to curb the unrelenting violence so their forces can start going home.
Vice President Adil Abdul-Mahdi's signature on an executive order opens the way for the much-delayed first session of the parliament which was elected on December 15.
It has also signalled fundamental disagreement within the once-unified majority Shi'ite ranks.
The constitution dictates that the first meeting be held no later than Sunday, but negotiations were still under way on a specific date.
The first session had been delayed by weeks of intense political infighting and reached an impasse after Abdul-Mahdi refused to sign President Jalal Talabani's decree on Monday.
The dispute centres around Shi'ite Prime Minister Ibrahim al-Jaafari's bid for a second term, which is opposed by a coalition of Sunni Arab, Kurdish and secular Shi'ite politicians.