Somalia’s interim Government teetered on the brink of collapse today after a Cabinet minister was assassinated as he left Friday prayers.

The embattled administration has already seen its limited authority dwindle in recent weeks as Islamic militias advanced across the country after seizing the capital Mogadishu.

Regional powers and western governments fear that the Union of Islamic Courts may turn Somalia into a haven for al-Qaeda. Several of its leaders have urged Somalis to launch a jihad against Ethiopian troops deployed in support of the government, as the country slips ever closer to all-out civil war.

In a turbulent 48 hours the transitional Government has been rocked by mass resignations and tomorrow the parliament is due to debate a motion of no confidence in the prime minister, Ali Mohamed Gedi, for allowing Ethiopians into the country and failing to secure peace.

That sense of political crisis heightened after today's murder of Abdallah Isaaq Deerow, Minister for Constitutional and Federal Affairs. Mohamed Guyo, an analyst with the Institute for Security Studies in Nairobi, said: "The transitional government is now in the process of total collapse.

"By Saturday I am expected it to have lost more ministers and it all shows that the decision to invite Ethiopian troops has fatally undermined the government."

With the transitional administration unable to wield power outside its stronghold of Baidoa, 150 miles from Mogadishu, it leaves the Union of Islamic Courts as the closest thing to a government in Somalia.

Eyewitnesses said Deerow was shot several times in the chest as he left a mosque in the government seat of Baidoa, about 150 miles from Mogadishu. Mohamed Abdi Hayir, Information Minister, said: "It looks like an organised assassination.

"So far we do not know who did it. They shot him as he was leaving the mosque then ran off."

Hundreds of people rioted in the streets of Baidoa soon after the news spread.

Deerow was seen as one of the Government’s political heavyweights and had been speaker in a previous parliament. He was close to both the President and the beleaguered Prime Minister and was known to be a keen supporter of inviting Ethiopian troops into Somalia.

"My feeling is that the people responsible are people within the transitional structures who believe that Ethiopian troops are a barrier to peace," said a Somali political watcher, who asked to remain anonymous for security reasons.

The transitional Government, formed in 2004, is the latest in more than a dozen attempts to bring peace to Somalia since 1991. Its position has looked increasingly fragile since June, when Islamist militias took control of Mogadishu, ousting an alliance of US-backed warlords.

The two sides have ratcheted up tensions in the past fortnight with a series of military manoeuvres.

First the Islamists, whose leader Sheikh Hassan Dahir Aweys is listed as a terrorist by the US, advanced to within 20 miles of Baidoa.

That prompted the deployment of Ethiopian troops around Baidoa and other key sites in an attempt to shore up the government of President Abdullahi Yusuf, a long standing ally of Addis Ababa.

While Ethiopia denies sending troops, its ministers have repeatedly warned that they would "crush" any Islamist attack on Baidoa.

Then Eritrean arms were flown openly into Mogadishu this week for the first time after months of secret shipments to the Islamists, in what appeared to be a deliberate challenge to the government.

The moves heighten fears that Somalia could become the scene of a proxy war between Eritrea and Ethiopia who fought a bitter border conflict from 1998 to 2000.

Meanwhile peace talks, which were due to resume in the Sudanese capital Khartoum on Tuesday, look unlikely to go ahead because Islamist leaders say they are not prepared to negotiate while foreign troops remain in the country.

The presence of Ethiopian troops has also split the Government, culminating in the resignations of 18 ministers — out of a cabinet of 102 — on Thursday. They accused their leadership of failing to engage in "national reconciliation".

With both sides rearming or reorganising their forces, it all means one thing for the war-weary people of Somalia — peace remains as far away as ever in their gun-ridden land.

Residents of Baidoa said that tension was growing day by day. "People are making sure that they have weapons at home," said an aid worker who asked not to be named. "MPs and ministers are not moving around as much as they used to, and everyone is staying in their houses more and more."

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