Al-Maliki, speaking at a ceremony on the 86th anniversary of the Iraqi army, reacted angrily to those who criticised the execution.
He said: "We find that this conduct is inciting sedition and flagrant interference in the internal affairs of Iraq and abuses feelings of the families of the victims."
A number of international leaders have criticised the manner of Saddam's hanging saying it appeared as a sectarian lynching rather than a court-directed punishment.
The criticism came after a guard, believed to be a Shia, taunted the Sunni former president in his final moments.
The strongest comments came from Hosni Mubarak, the Egyptian president, who said that the execution had turned Saddam into a "martyr."
New security plan
In a separate development, al-Maliki said that Iraqi forces would launch a new effort, with US help, to wrest control of Baghdad's neighbourhoods from armed groups.
Al-Maliki said: "The Baghdad security plan is now ready and we will depend on our armed forces to implement it with multinational forces behind them. Field leaders will ask for help from these forces if needed."
Iraqi forces will begin a neighbourhood-by-neighbourhood assault on fighters in the capital this weekend, as a first step in the new White House strategy to contain violence in the capital.
The first details of the plan emerged on Friday, a day after George Bush, the US president, and al-Maliki spoke for nearly two hours by video conference.
Bush is expected to outline more of the strategy in the coming days.
On Saturday, Iraqi police clashed with armed men in the area near Haifa Street, a traditional Sunni area in central Baghdad, when they went to investigate a report that 27 bodies had been found.
A source at Baghdad police headquarters said local police called in reinforcements, but when they arrived, they came under fire.
Meanwhile, police said two car bombs killed four civilians in separate attacks in the Iraqi capital on Saturday.
A parked car exploded near a fuel station in the southern neighbourhood of Dora at midday, killing three people and wounding four others.
Another car bomb targeted the convoy of a high-ranking Iraqi police officer in the central Baghdad neighbourhood of Karradah, killing a pedestrian and wounding six.
Ali al-Yassiri, head of emergency police in the Iraqi capital, survived the attack on his convoy, while three of his bodyguards were hurt.