The attack, which followed a similar operation last December, illustrates the impunity with which militants in Iraq can strike even targets that should be highly secure, as the country suffers its worst violence in years.
Two bombers dressed in police uniforms shot dead a policeman and took control of the council headquarters with employees inside, a police lieutenant colonel said.
Clashes broke out between the militants and security forces, and a suicide bomber detonated an explosives-rigged vehicle near police and Sahwa anti-Al-Qaeda militia forces when they arrived at the scene.
The three blasts wounded a total of 47 people, mainly security forces.
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A doctor from a local hospital confirmed that the assault killed five people and wounded 47, among them the deputy head of the city council.
The attack in Samarra follows a similar incident in Tikrit, another city in the Sunni-majority Salaheddin province, north of Baghdad, in which militants detonated a car bomb and seized the city council headquarters on December 16.
The following week, on December 23, suicide bombers attacked the headquarters of a local television station in Tikrit, killing five journalists.
Salaheddin province is also home to the Sulaiman Bek area, where militants repeatedly battled security forces for control last month, leaving dozens of people dead.
Attacks in other areas of Iraq killed three security forces members today -- a Sahwa militiaman in Kirkuk province and two policemen in Nineveh province.
The year-long surge in violence in Iraq has been driven by widespread discontent among the minority Sunni Arab community, and by the bloody civil war in neighbouring Syria.
The Iraqi government also faces a two-month crisis in Anbar province, west of Baghdad, where it has lost all of the city of Fallujah as well as shifting parts of provincial capital Ramadi to anti-government fighters.
It is the first time anti-government forces have exercised such open control in major cities since the peak of the deadly violence that followed the US-led invasion of 2003.
More than 1,770 people have been killed in attacks and clashes in Iraq since January 1, according to AFP figures based on security and medical sources.