Somalia's interim prime minister has asked for international help against the "al-Qaeda" and "terrorist" expansion in the country.
Fighters seized control of the capital Mogadishu in June
Ali Mohamed Ghedi appealed for aid soon, before it was too late.
He was speaking after his Islamist rivals seized the key port of Kismayo, where they fired at demonstrators, reportedly killing three people.
The Union of Islamic Courts deny having any links to al-Qaeda and say they are bringing security to a lawless country.
"I would appeal to the governments of the region to join our efforts and protect the region from the expansion of this al-Qaeda network, these terrorists," Mr Ghedi said in neighbouring Kenya.
He also said the takeover of Kismayo was a "violation" of the ceasefire agreed between the UIC and the government in Sudan.
Meanwhile, eyewitnesses report that hundreds of Ethiopian troops have crossed the border, heading for Baidoa - the only town controlled by the internationally recognised government.
Ethiopia supports the administration of President Abdullahi Yusuf but has denied that its troops are in Baidoa.
The foreign secretary of the Union of Islamic Courts (UIC), Ibrahim Hassan Addow, told the BBC there was "no question" that Ethiopian forces were deep inside Somalia.
He said the UIC would defend Somali territory against Ethiopian troops.
Mr Ghedi's government only controls a small part of Somalia, around the town of Baidoa, while the UIC has expanded across most of the south.
They seized Kismayo on Sunday without a fight, after gunmen loyal to Mr Ghedi's Defence Minister Barre Hiraale fled the town.
After the takeover, pro- and anti-UIC rallies were held.
Islamist guards opened fire after some residents burnt tyres, chanted anti-Islamist slogans and threw stones.
An MP told the BBC's Somali service that three people had died. Some of the protesters had been seen burning Islamic head-dresses.
UIC officials say the protests were organised by those who opposed their ban on the popular stimulant khat during the Muslim holy month of Ramadan.
An Islamist leader spoke at an earlier rally which passed off peacefully.
Earlier this month, the African Union agreed to a request by Somalia's transitional government, to send in a regional peacekeeping force.
Kismayo had been seen as a possible landing point for the peacekeepers.
Witnesses told AFP news agency they had seen more than 600 Islamist gunmen on about 50 "battlewagons" - machine-gun mounted pick-ups also known as "technicals" - heading toward Kismayo on Sunday.
Thousands of people are reported to have fled the city in recent days.
Earlier reports said that thousands of people had gathered in the town, chanting "God is great" to welcome the UIC fighters.
The UIC has steadily increased its hold on Somalia since its fighters took control of the capital, Mogadishu, in June, taking control of hundreds of square kilometres of territory while hardly firing a shot.
Mr Ghedi's government was set up in 2004 after more than two years of talks designed to give Somalia its first effective national government since 1991.