"We are working on reshuffling the ministry's vital posts like [the leaders of the] police commandos and public order forces, as well as some under-secretaries," Abdul-Karim Khalaf, an interior ministry spokesman, said on Saturday.
Khalaf also said that the ministry had fired 3,000 employees accused of corruption or human rights abuses since May. Up to 600 of them will face prosecution.
The Shia-dominated police force is widely accused of having links to militia forces and death squads, which have been blamed for the killings of Sunni Muslims.
Earlier this month, an entire brigade of about 700 policemen were suspended from service and returned to their barracks because of suspected militia sympathies. The commander of one of the brigade's battalions faces criminal prosecution and others are being investigated.
The troops were suspected of letting Shia militias carry out the mass kidnapping of about two dozen people from a frozen food factory in Baghdad, at least seven of whom have since been found dead.
But Khalaf played down the role of the ministry's police forces in militia violence, blaming the Facilities Protection Service instead. The FPS, created to guard government buildings and infrastructure, has some 150,000 members but an unclear command structure.
The FPS "is part of the problem in the death squad activities. They are not working under the supervision of either the interior or the defense ministry but under the ministries that use them", Khalaf said.
Bolani was brought in partly
because he has no militia links
US commanders have also said that FPS members may be carrying out a large portion of the death squad killings.
When the current government was formed in May, Jawad Bolani, the interior minister, was brought in partly because he had no links to the Shia or Sunni militias. But his lack of militia connections appears to have worked against him as he has less power to bring about change.
Authorities are currently investigating the killing of Colonel Salam al-Maamouri, the commander of an police unit which was tackling both Sunni fighters and Shia militias.
Al-Maamouri was killed along with an aide in his office in the southern city of Hilla when a bomb exploded. Khalaf said the assassins appeared to have had help from "elements inside his office".
In another development, Saudi Arabia's king has met prominent Iraqi Sunni and Shia clerics in Makka and urged them to seek an end to the violence.
"May your country live in peace and pacification; my brothers, we need now patience, calmness and quietude to get to know each other," King Abdullah said, according to the statement.
A prominent anti-government Iraqi Sunni cleric, Harith al-Dhari, who leads the influential Association of Muslim Scholars, was among those who met with King Abdullah.
Al-Dhari has expressed his readiness to meet with top Shia religious leaders, part of an initiative to curb sectarian violence.
Saudi Arabia, along with many other countries in the region, is worried about the prospect of civil war in Iraq in its neighbour.