Sheikh Abdirahim Isse Adow, the spokesman for the Islamic Courts Union (ICU), said: "We have great sympathy for the innocent civilians who are being killed."
There was no immediate comment from the Ethiopians.
The ICU, a group which had taken control of large areas of the country in opposition to the interim government, was driven out of Mogadishu in 2006 when the government brought in Ethiopian forces to help them fight.
The ICU and several other anti-government groups and splinter groups still remain in the Horn of Africa nation.
Pressure and urgency
Anti-government fighters, who now control most of southern Somalia, mount daily attacks on the Western-backed government and its Ethiopian supporters.
Analysts say it will be hard for them to take control of Mogadishu while heavily armed Ethiopian forces remain stationed there.
Meanwhile, Ethiopia has said its troops will withdraw from the country by the end of 2008.
The announcement puts pressure on Somalia's interim government and adds urgency to its long-standing request for international peacekeepers.
Fighting in Somalia has killed 10,000 civilians since early 2007, driven more than a million from their homes and left more than three million Somalis in need of emergency food aid.