Sheikh Abdurrahman Ibrahim Ma'ow, the chairman of the Council of Islamic Courts in the Somali region of Hiraan, where witnesses reported seeing Ethiopian troops, urged them to leave.
"We, the authorities in the region, will not accept it," he said by telephone.
"If they do not leave within 24 hours we will fight with them."
Somalia's Transitional Federal Government (TFG) requested the deployment of Ethiopian troops in December 2006 to remove the Union of Islamic Courts (UIC), that had controlled southern Somalia and the capital Mogadishu for six months.
The UIC and other armed anti-government factions then launched a battle with government forces and Ethiopian troops which had killed thousands of people.
The last Ethiopian troops withdrew on January 25 in a move widely welcomed by Somalis who had viewed the troops as an occupying force. However, their withdrawal has sparked fears of a security vacuum in the country.
An African Union (AU) peackeeping force remains inside the country, consisting of Ugandan and Burundian troops. It has been in Mogadishu for about two years and is charged with protecting key government installations.
Somalia and Ethiopia have been rivals for decades, and fought in the late 1970s over a southeastern region of Ethiopia populated principally by people of Somali origin.
Earlier al-Shabab, an armed anti-government group, called on Somalis to intensify their war against AU troops, aimed at driving the peacekeepers out of the country.
|Al-Shabab has vowed to fight all foreign
forces inside Somalia [AFP]
"We call on the African forces to pull out of our country or face resistance harsher than what they have ever experienced," Sheikh Mukhtar Robow, a leader of al-Shabab, told AFP news agency on Tuesday.
Robow was speaking to reporters in the town of Baidoa, a day after Somali officials accused AU soldiers of killing 18 civilians in Mogadishu.
"We are telling them that we don't need their help if they are going to be massacring our people and I urge all holy fighters in the country to step up their struggle against them," Robow said.
Somali officials said at least 18 people were killed by AU troops on Monday when they opened fire on three minibuses after a roadside bomb targeted their convoy in southern Mogadishu.
Abdifatah Shaweye, the deputy mayor of Mogadishu, said more than 20 civilians were killed in the shooting.
"The African Union forces committed mass killings today after an explosion hit their convoy. The number of innocent civilians they killed after the explosion exceeded 20," he said.
Major Bahuko Baridgye, a spokesman for the AU forces, denied the charges and said that three civilians died and four others were wounded in the explosion.
"The information we got indicates that three civilians died in the explosion and one of our soldiers was lightly injured. The vehicle was also slightly damaged," Baridgye said.
"Our forces did not open fire on people."
AU peacekeepers have often been targeted by anti-government fighters since the first Ugandan contingent was deployed to the country in March 2007.