Following their defeat in Baladweyne, leaders of the Islamic courts called on the Ethiopian troops to withdraw.
Sheikh Mohamed Ibrahim Bilal, a senior Islamic commander, said: "We call on the international community to act soon about this violation."
Both sides have reported killing hundreds of their opponents in the recent fighting, but the claims could not be independently confirmed.
Ethiopia bombs airports
|Baidoa is the only major town controlled by Somlia's interim government|
Also on Monday, Ethiopian fighter jets bombed the airports of Mogadishu, the Islamist-held capital, and Baledogle, Somalia's largest military airfield 100km to the west.
Ibrahim Hassan Adow, the foreign secretary of the Islamic Courts Union, told Al Jazeera that the bombing of Mogadishu by Ethiopian MiG aircraft injured two people, one of whom was a cleaner.
"Ethiopian attacks against Somalia have no limits. It seems the entire world is silent about it."
Ethiopia said it bombed the airport in order to halt the supply of arms to the courts.
Solomon Abede, the Ethiopian foreign ministry spokesman, said: "It was attacked because illegal flights were attempting to land there.
"It was also reported that some of the extremists were waiting for an airlift out of Mogadishu."
In November, a UN arms-monitoring group reported that flights originating in Eritrea, Saudi Arabia, Iran, Djibouti and Syria landed in Mogadishu and Baledogle.
The UN and the Somali government said that many of the flights carried arms and military supplies for the Islamic Courts. The US has also been accused of funding and arming those fighting for the government.
|The Islamic courts guard Mogadishu's|
airport after the air raid [Reuters]
The Somali government said that it was closing the country's borders.
This is little more than a symbolic measures as the government controls little more than the town of Baidoa while the country's long borders are largely unmarked.
However, aid agencies said they feared that the measure would hamper their attempts to send food and medical supplies into the poverty-stricken country.
The UN World Food Programme airlifted more than 14 tons of food into Somalia on Monday, but had not yet been notified of any border closures, Peter Smerdon, an agency spokesman, said.