Fighting raged in Najaf and Baghdad on Wednesday, while unconfirmed reports suggested clashes in Basra too.
In Baghdad al-Sadr followers seized three offices of the Supreme Council for Islamic Revolution in Iraq (SCIRI) in Baghdad.
Heavy fighting broke out between the followers of the two rival parties in al-Habibiya near Sadr City, east of Baghdad.
"Five people were killed, some of them are followers of al-Sadr, and seven others were wounded in the clashes," said Saheb al-Amiri, general secretary of Shahid Allah (God's Martyr), an organisation linked to al-Sadr's movement.
Aljazeera quoted Jalil al-Nouri, information director at al-Sadr's office in Najaf, as saying that a number of people had been killed and injured in the clashes in the city between Iraqi police personnel and al-Sadr supporters.
Several explosions were also heard in Sadr City, while loudspeakers in local mosques announced that the Najaf clashes were the work of the Badr Organisation, formerly known as Badr Brigade the military wing of SCIRI, formed in Iran in 1982.
However, Hadi al-Amry, secretary-general of the Badr Organisation, denounced the attack on Najaf's al-Sadr Martyr Office and called for an investigation into the incident as well as for bringing the culprits, whoever they might be, to justice, according to Aljazeera.
Al-Amry said that the Badr Organisation had nothing to do with Wednesday's incident, and that it considered it an attack against its own offices.
Nevertheless, supporters of al-Sadr announced they were suspending their membership of the cabinet in protest against the Najaf attack.
Twenty-one lawmakers and one cabinet minister allied with al-Sadr will refuse to carry out their duties indefinitely, al-Sadr ally Fattah al-Sheik said on Wednesday.
Transport Minister Salam al-Maliki confirmed the move and said he had suspended his membership in the cabinet in protest against the burning of al-Sadr's office in Najaf.
Al-Sadr's movement now has
representation in Iraq's cabinet
The move could complicate efforts to convene parliament to vote on a new constitution and raises fears of internal conflicts among the Shia at a time when Sunni Arabs are outraged over the new draft constitution.
"We condemn the shameful attack on our office in Najaf and know it is the work of Badr Organisation, which came back to Iraq on American tanks," a member of al-Sadr's group announced at a local mosque in Sadr City.
Interior Minister Bayan Baker Solagh - a senior SCIRI member - confirmed the Najaf clashes and said that demonstrators "burnt down the office of al-Sadr's group".
"There was a clash between demonstrators ... and defenders of the office," Solagh told the state-owned Iraqia television.
Al-Sadr launched two uprisings in 2004 against US forces from the Imam Ali shrine, in which hundreds of his supporters were killed.
Al-Sadr himself assumed a low profile following the uprising, reportedly going to study Koranic texts, while his militia was largely disarmed in a US-backed cash-for-weapons programme.
Prime Minister al-Jaafari has
appealed for calm
While much of the militia's heavy weaponry was handed over, most held on to their small arms.
Al-Sadr re-emerged on Iraq's tempestuous political scene in April, saying that the fight to get US troops out of the country was now purely political.
On Friday, thousands of his supporters marched in Baghdad in protest against federalism in Iraq's new constitution, which is due to be put to MPs on Thursday.
Prime Minister al-Jaafari, a Shia himself, appealed for calm in Iraq.
"I will send a group of my brothers to investigate (the situation) ... . I call upon the residents of Najaf to spread peace ... . We will not accept going back to arms" to settle issues, he said on the Iraqia network.
The clashes came just a few hours after at least 35 people were killed in clashes across central and northern Iraq.
On the positive side for the government, the Kurdistan Parliament has backed the draft constitution handed over to the national assembly in Baghdad.
The endorsement came in a special session held by the parliament in Arbil. Some parliament members expressed reservations, though, over what they called missing points in the constitution, foremost of which is federalism.
Heavy fighting broke out between dozens of Iraqi fighters and Iraqi police in western Baghdad, police and witnesses said.
"We condemn the shameful act to attack our office in Najaf and know it is the work of Badr Organisation which came back in Iraq on American tanks".
A member of al-Sadr group
Around 50 men armed with AK-47s and rocket-propelled grenades attacked a police station in al-Rabei street, west of Baghdad, in a show of force by fighters who do not recognise the US-backed Iraqi government.
Police said 10 civilians and three policemen were killed.
Iraqi police sent for back-up from the US army.
Aljazeera reported that 15 people, including three Iraqi policemen, were killed and 59 others injured in three attacks using booby-trapped cars driven by bombers that targeted Iraqi police patrols in western Baghdad's al-Jamaa neighbourhood.
A group of armed men launched an attack against a police station immediately after the three car bomb blasts, Aljazeera added.
In another incident, a deputy of the Iraqi justice minister, Yosha Ibrahim, escaped assassination, but four of his guards were killed and five wounded in an attack by armed men on his convoy in western Baghdad, police said.
It was the second attempt on his life in 48 hours.
Separately, four Iraqi people were killed and seven were wounded when fighters attacked their bus in Khalis, 75km north of Baquba.
Police said the dead were Shia Muslim pilgrims returning from a visit to holy shrines in Iran.
Four mortar rounds landed on a base used by the Iraqi police's Rapid Reaction Force in Baquba, 65km northeast of Baghdad, wounding seven.
Police said most of those wounded were recruits, but said a young girl and a child were also injured.
US soldiers came to the aid of
Iraqi police in western Baghdad
Aljazeera reported quoting the information director of the Association of Muslim Scholars, Muthana Harith al-Dhari, that US soldiers backed by Iraqi National Guard personnel raided the house of Shaikh Harith al-Dhari, the association's secretary-general, in Khan Dhari district.
The soldiers searched the building without causing any damage. Sheikh Harith al-Dhari was not in his home at the time of the raid, Aljazeera reported quoting Muthana.
On Tuesday, an Iraqi soldier was killed and another wounded when two mortars landed on a checkpoint at Musayyib, south of Baghdad, police said.