In the end, Mogadishu’s feared Islamic militias simply melted away. Young fighters, some forced to swap schoolbooks for AK47s in recent months, had no stomach for a fight with an Ethiopian war machine that had helped Somali government troops to the outskirts of the capital. They discarded their fatigues, took off their Islamic caps and transferred their allegiance back to their clans.

Muhammad Ismail 24, was among the militiamen who stayed at home. “It looked like the courts were losing so I decided last night that I should go back to my clan. They are the only ones who can protect me and pay me now,” he said.

The leaders of the Union of Islamic Courts fled the city late on Wednesday, turning over arms and ammunition to local clan leaders. Government technicals — pick-ups mounted with heavy machine-guns — rolled into the city without meeting resistance yesterday.

Analysts said that the departure of the courts left a dangerous political vacuum and residents feared a return to the 15 years of anarchy — fuelled by clan rivalries — that ended with the rise of the Islamists last June. “Things here are very tense now,” Abdiaziz Adow, a shopkeeper, said by telephone. “No one wants things to go back to the way things were but we have already heard about people being shot and all the shops are closed.”

The government forces arrived to a mixed reception. While some residents waved flowers and cheered the arrival of soldiers promising to maintain order, others said that Ethiopian stooges were not welcome. Mogadishu reverberated to the echo of gunfire as gunmen looted buildings used by the courts or settled old scores. It was a grim reminder of the way it used to be before the Islamists imposed their idea of law and order on a city damaged by years of thuggery.

The city’s port, airport and presidential palace were all seized by militia leaders. Muhammad Jama Furuh had handed his seaport over to the Islamists six months ago. Yesterday the warlord ordered his personal militia into the port but insisted that it was only for safekeeping. “The port is now in my hands. I want to provide security and protect it from looting . . . until we hand it over to any other administration,” Furuh said. Meanwhile, government and Ethiopian troops assembled 13 miles (20km) outside the city in the town of Afgoye. Ali Mohamed Gedi, the Somali transitional Prime Minister, arrived there by Ethiopian helicopter and said that his officials would enter Mogadishu today. “Today is a historic day for Somalia. It is a day of reconciliation and victory (and) a day of the return of law and order,” he said, during a break in talks with clan elders. “This victory is Somali people’s victory. We are here to bring peace.”

Ethiopian aircraft began bombing Islamist targets on Sunday and followed up with a raid on Mogadishu airport on Christmas Day. By Wednesday night Somali government officials were telephoning clan elders in Mogadishu, urging them to remove their backing for the courts.

Before evacuating Mogadishu, the leader of the courts’ executive council told reporters that his movement was handing the city back to the clans. “We have withdrawn our forces and there are no Islamic court forces (there). It is the Somali people who are resisting,” Sheikh Sharif Ahmed said. “We did not leave the capital to chaos. We left it to avert heavy bombing because Ethiopian forces are practising genocide against the Somali people.”

Observers said that attention must now focus on setting up an administration that can govern the country. Matt Bryden, consultant to the International Crisis Group, which monitors conflict, said that a quick political solution was vital. “The risks are that if Ethiopia and Somalia are unable to consolidate their military victory politically then we are back at square one with the conditions that gave rise to the courts in the first place.”

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