However the Somalian government accused the Islamists of lying about an Ethiopian troop incursion as a pretext for attacking the government's headquarters in the town of Baidoa.
Sheikh Shariff Sheikh Ahmed, the head of the Joint Islamic Courts, said on Sunday that he had "confirmed" that 300 Ethiopian troops crossed into southwestern Somalia early on Saturday to counter his increasingly powerful group.
"We ask them to go (back) to their country, if not their presence will cause a big conflict between the invaders and Somali people," Ahmed said.
The Ethiopian government denies its troops have entered Somalia, saying it had boosted troop levels along the Somali border following provocation from Islamists.
A spokesman for the Ethiopia-backed Somali government said the Islamists accusation was "absolutely baseless".
"There are no Ethiopian troops in Somalia. We have received intelligence reports that they are using the incursion lies as a pretext to attack Baidoa," said Abdirahman Nur Mohamed Dinari, a government spokesman.
"But our army, militia, police and forces are ready to defend the city should they dare attack," he added.
Antonio Guterres, the head of the UNHCR - the United Nations refugee body - said the violence in Somalia risked causing a humanitarian crisis in Somalia.
Ethiopia has been a strong supporter of the interim Somali government led by President Abdullahi Yusuf.
Earlier this month the Islamic courts defeated a coalition of militia leaders - said to be backed by the US - that have run the country since the collapse of central government in 1991.
The fighting has killed around 350 people since February.