It is unclear who currently has the upper hand in Basra |
So far more than 40 people have died and some 225 have been injured over the two days of clashes in Basra.
Fighting is also continuing in Baghdad, and there have been casualties after rockets were fired at the Green Zone.
Prime Minister Nouri Maliki has given militants 72 hours to lay down their arms or face "severe penalties".
His campaign to "re-impose law" in the city triggered unrest elsewhere in Iraq, and many towns are under curfew.
Unrest in Basra has been stoked by a variety of militias and criminal gangs.
But the government's unspoken intent is to stop it falling under the sway of the Mehdi Army, led by the radical young cleric Moqtada Sadr, BBC Middle East analyst Roger Hardy says.
Clashes continue
After an overnight lull, the fighting resumed in Basra on Wednesday.
The AFP news agency quoted witnesses in Basra as saying the fighting was concentrated on the districts of Gazaiza, Garma, Khmasamene, Hayania and Maqal.
BASRA KEY FACTS Third largest city, population 2.6 million approx Located on the Shatt al-Arab waterway leading to the Gulf - making it a centre for commerce and oil exports Region around city has substantial oil resources 4,000 UK troops based at international airport |
Medical officials say 46 people have been killed in the fighting, along with 225 hurt. A Basra city council member said there were few civilian casualties as they were staying inside their houses.
A large number of gunmen have been detained, say officials.
Reports suggest that the fighting is not on the same scale on Tuesday but, where there was no fighting, Basra's streets remained deserted even after the night curfew ended at 0600 (0300 GMT).
British forces, which patrolled Basra for nearly five years, withdrew to a base outside the city in December and have not been involved in the fighting.
In Baghdad, rockets were fired at the Green Zone, the diplomatic and government compound.
Five Iraqi civilians were killed by stray rockets, while inside the heavily fortified zone three Americans were seriously injured.
In Sadr City, a vast Shia suburb in the capital, there were overnight clashes between Mehdi Army fighters and American and Iraqi soldiers.
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Twenty people died in the violence and at least 115 people have been injured, according to police.
Here and in other Shia areas of Iraq, many shops and offices are shuttered, indicating Moqtada Sadr's call for a campaign of civil disobedience is being followed.
One report also suggests hundreds of people are demonstrating in Sadr City.
More clashes also broke out in Kut, south-east of Baghdad, where two people were reported dead on Wednesday.
In a separate incident, US forces battling suspected al-Qaeda insurgents in the northern town of Tikrit say they injured or killed "several Iraqi civilians" in an airstrike.
Iraqi sources say at least five are dead, including a judge.
Ultimatum
In a statement, Mr Maliki gave militants a 72-hour deadline to lay down their arms and sign a pledge renouncing violence.
In Sadr City, shop owners inspected damage done overnight |
"Otherwise, they will face the most severe penalties," he said in the statement which was broadcast by state television.
The Basra operation is being personally led by Mr Maliki, a fact hailed by Washington as "brave".
Sadrists are convinced the operation is an attempt to weaken them ahead of provincial elections due in October, but Mr Maliki has embarked on a risky strategy, says the BBC's Roger Hardy.
For one thing, it is far from clear that it will succeed.
The Sadrist movement enjoys widespread support, especially among the young and the poor, and is well entrenched in Basra and many other predominantly Shia towns and cities in the south.
For another, if the ceasefire which the Sadrists have largely followed since last year were to collapse, that would seriously undermine claims by the government - and by the Bush administration in Washington - that Iraq was moving from civil war to political reconciliation, our correspondent says.
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