Ethiopia has sent up to 15,000 additional troops into its Horn of Africa neighbour as it struggles to pacify an Islamist-led insurgency.

Entire districts have emptied as people have been forced from their homes. Mogadishu's mayor, Mohammed Dheere, told residents on Sunday that they should leave. Diplomats in Nairobi have warned that the Ethiopian attacks, targeted at certain sub-clans opposed to the government, could be considered ethnic cleansing.

The UN's humanitarian co-ordinator, Christian Balslev-Olesen, said there were "reports of house-to-house searches and large-scale detentions," which have "created a climate of fear among the population not witnessed before".

Ethiopian troops and Islamist insurgents were engaged in three major battles over the weekend that left about 100 civilians injured.

"You see groups of people spontaneously protesting, crying for help from the international community and wondering how long Mogadishu will keep on being destroyed," the UN refugee agency quoted a staff member in Somalia as saying.

About 46,000 of those fleeing have gone to the town of Afgooye, 20 miles outside Mogadishu, where there are already more than 100,000 people displaced from fighting earlier this year. Aid agencies warned yesterday that they were unable to provide any assistance because of chronic insecurity. Armed checkpoints, the scourge of Somalia since its last central government was overthrown in 1991, are proliferating at an alarming rate. Militias aligned to one of the 100 or so different sub-clans set up checkpoints, demanding money from all who pass.

Humanitarian convoys carrying food or water can be charged up to $100 (£50) a time. It is estimated there are more than 200 checkpoints on the roads leading into Mogadishu.

Paul Smith-Lomas of Oxfam said aid agencies were "extremely concerned that a humanitarian catastrophe is unfolding and agencies are unable to get safe access to tens of thousands of people fleeing Mogadishu."

Harassment of UN and aid agency staff members is also on the rise. The six remaining international UN staff in southern and central Somalia were evacuated from Merka, a town 45 miles south of Mogadishu, on Sunday.

Earlier this month, the World Food Programme's senior officer in Mogadishu was arrested in an armed raid on the UN compound carried out by the government's own security forces.

Mr Balslev-Olesen said it was "very likely" many of those displaced in April would begin to die. "We have not even been able to provide the basic needs for these people in terms of water and sanitation," he said. "Unless we get access, people will start dying."

Ethiopia invaded Somalia in late December last year, driving out the Union of Islamic Courts, which had taken control of Mogadishu and large areas of southern and central Somalia. A transitional government, which had previously been holed up in a small western town, Baidoa, was instantly installed in Mogadishu.

Ethiopia was given tacit approval for the invasion by the United States, which wanted to target terrorist suspects it believed were in Somalia. The US views Somalia as a vital front in the global "war on terror" and has carried out its own air strikes in the country.

But things have not gone as planned. Although the Courts were defeated within days, it took less than a month for fighters fromal-Shabaab, the hardline wing of the Courts' militia with links to al-Qa'ida, to begin an insurgency.

Somalia's interim government has struggled to keep control of the country, relying on thousands of Ethiopian troops. Longstanding animosity among ordinary Somalis towards Ethiopia has drained the government of what little public support it had, particularly in Mogadishu, which is a stronghold of the Hawiye clan.

The government, headed by Abdullahi Yusuf, is dominated by members of his Darod clan.

A long-running feud between President Yusuf and his Prime Minister, Ali Mohamed Gedi, has also damaged the government. Mr Gedi resigned from the government earlier this week after pressure from the United States, where he and his family have been offered asylum.

"The Ethiopians are in way over their heads," said one Western diplomat. "They can't cope any more and are looking desperately for an exit strategy."

Ethiopia had hoped that the African Union (AU) would provide their exit strategy. A force of 8,000 AU troops was sanctioned earlier this year. If fully deployed, it would have enabled Ethiopia to withdraw.

But so far just a single battalion of 1,600 Ugandan soldiers has been deployed. A battalion of Burundians is expected to join them later this month, but their deployment has been beset by operational difficulties.

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