Basra erupted yesterday into some of the heaviest fighting since it was seized by the British Army five years ago, as Iraqi government forces took on a Shia militia that has turned the city into a morass of murder, kidnap and oil smuggling.

Nouri al-Maliki, the Shia Prime Minister, who has worked in often awkward collaboration with the militias, flew into the southern port city to take personal charge of the mission, staking his reputation on a showdown with the all-powerful al-Mahdi Army.

There were further clashes in other cities in the south and in areas of Baghdad as the sprawling militia hit back, ordering policemen out of neighbourhoods they control and even kidnapping officers.

After the US military’s success in curbing a Sunni insurgency and turning guerrillas against allies linked with al-Qaeda, the Government decided to take on the Shia militia that dominates the south and centre of the country, and which has infiltrated the police force, ministries and the civil service.

Iraq timeline: five years of conflict

From accusations that the weapons of mass destruction dossier had been sexed-up to withdrawal of British troops from Basra

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The fighting quickly spread from Basra to the town of Kut, just southeast of Baghdad, and to parts of the capital, where supporters of Hojatoleslam Moqtada al-Sadr, the vitriolic anti-American cleric who founded the militia, demonstrated and staged strikes against the government crackdown.

The fighting in Basra, where around 80 per cent of Iraq’s oil is located, was the biggest battle the al-Mahdi Army has fought since weathering a US military onslaught in the holy city of Najaf in 2004. Then, however, it rallied massive support by branding itself as resistance to the US military occupation. Now, after years of murders, extortion, and racketeering by the militia, any such rallying cry is unlikely to stand close scrutiny.

Al-Mahdi Army does, however, have a vast, loose network of supporters and members in key areas of society, notably the police force. A source at the Interior Ministry said there had been chaos for several hours as various bureaux beholden to different political factions issued countermanding orders yesterday.

The Basra offensive was launched by the army, a more loyal government force that has been the focus of US military training and is considered to be much less influenced by militias, many of which receive support from Iran. Major-General Ali Zaidan, the commander of the Iraqi army operation, said the offensive would continue “until we achieve our target”. That target was to “wipe out all the outlaws. There were clashes and many outlaws have been killed,” he said. At least 22 people were killed in the fighting, officials said, as British helicopters provided reconnaissance in Basra and US warplanes flew over Sadr City in Baghdad, a hotbed of the militia.

British troops were not involved in the fighting itself. They withdrew from Basra late last summer to an airbase on the edge of city.

Even before that, however, they had largely handed over control of Basra to Iraqi forces even as militias were taking over. With troop numbers due to be cut to just 2,500 by the end of the spring, some critics say there are barely enough soldiers in the base to protect their own operations.

After touring Basra on Monday, Mr al-Maliki promised a crackdown on militias that were waging a “brutal campaign . . . accompanied by the smuggling of oil, weapons and drugs . . . Basra has become a city where civilians cannot even secure their lives and property”.

In an ominous sign that the unrest could intensify, Hojatoleslam al-Sadr threatened a countrywide civil revolt. Officials reported al-Mahdi Army fighters in Sadr-controlled areas of Baghdad kidnapping policemen affiliated to a rival militia, the Badr Brigades, the armed wing of the Supreme Islamic Iraqi Council, which is a senior government party.

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