MOGADISHU, Dec 28 (Reuters) - Triumphant Somali government forces and their Ethiopian allies marched into Mogadishu on Thursday after Islamist rivals abandoned the war-scarred city they held for six months.

The flight of the Islamists was a dramatic turn-around in the volatile Horn of Africa nation after they took Mogadishu in June and spread across the south imposing sharia rule.

Terrified of yet more violence in a city that has become a byword for chaos, some Mogadishu residents greeted the arriving government troops, while others hid.

"People are cheering as they wave flowers to the troops," said resident Abdikadar Abdulle, adding scores of government military vehicles had passed the Somalia National University west of the city centre.

Parts of Mogadishu shook with the sound of gunfire and there were outbreaks of looting after leaders of the Somalia Islamic Courts Council (SICC) fled its base early in the morning. Some fighters ditched their uniforms to avoid reprisals.

"We have been defeated. I have removed my uniform. Most of my comrades have also changed into civilian clothes," one former SICC fighter told Reuters. "Most of our leaders have fled."

The fall of Mogadishu came about 10 days after the Islamists sought to march on the government base of Baidoa. That prompted Ethiopia to come openly into the war, proving the decisive factor in saving the government and pushing back the Islamists.

The SICC had brought a semblance of stability to Mogadishu after chasing U.S.-backed warlords from the city in June. Residents said order had collapsed with their departure.

"Mogadishu is now in chaos," Islamist leader Sheikh Sharif Ahmed told Al Jazeera television.

WARLORD FEAR

Islamist defence lines were routed by a joint force of Ethiopian armour and government fighters. But SICC leader Ahmed said his side's hasty withdrawal was a tactical move and analysts say the Islamists could still wage a guerrilla war.

Ethiopian Prime Minister Meles Zenawi vowed to pursue the Islamist leaders. "We will not let Mogadishu burn," he added.

While the African Union (AU) has called for him to withdraw his forces "without delay", Meles is believed to have the tacit support of Washington in his push against the Islamists.

More than a week of mortar and rocket duels between the Islamists and the Ethiopian-backed government spiralled into open war 10 days ago.

The U.N. refugee agency said on Wednesday thousands of people had fled and were in a "desperate situation". On Thursday it said at least 17 people died and about 140 were missing after boats in which they were fleeing capsized off Yemen.

With Eritrea accused of backing the Islamists, many had feared the conflict would engulf the Horn. Ethiopia, like the United States, says the Islamists are supported by Al Qaeda. It says it has taken foreign prisoners and killed radicals from abroad, including some with British passports.

U.N. experts have accused 10 nations of providing arms, expertise and men to both sides. An al Qaeda-backed group in Iraq posted a statement on the Internet this week urging Muslims to support the Islamists.

The SICC has depicted the conflict with Christian-led Ethiopia, which has one of Africa's most effective armies, as a holy war against "crusaders", tapping into decades of cross-border rivalry.

Government spokesman Abdirahman Dinari said the Islamists had fled to the southern port city of Kismayu and the administration controlled 95 percent of the country.

Somali Prime Minister Ali Mohamed Gedi flew to a town near the capital on Thursday afternoon.

YEARS OF CHAOS

Ahmed said the Islamists were united and determined to push out Ethiopian forces, but retreated to avoid more bloodshed.

By fleeing, the Islamists appeared to have averted the risk of becoming embroiled in the fierce street fighting that forced the U.S. military from Mogadishu more than a decade ago in a humiliating episode captured in the film "Black Hawk Down".

Dinari said President Abdullahi Yusuf remained in the government's south-central base Baidoa. But Prime Minister Gedi landed at Afgoye in an Ethiopian military helicopter, some 30 km (19 miles) west of Mogadishu, where he was met by cheering crowds and clan leaders from the city.

"Our forces are controlling the situation," he said.

The return of the government to the capital would be a huge step in achieving greater legitimacy in the 14th attempt to restore central rule since the 1991 ouster of a dictator.

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