Meles said Ethiopian forces had been "trying to inflict the biggest losses" on the UIC fighters to guarantee that they would not re-group after the withdrawal.
"We have concluded all combat operations," he said.
The UIC fighters abandoned Mogadishu, the capital, last week in the face of advancing Ethiopian and government forces. They said their retreat was tactical and designed to avoid major bloodshed.
Also on Friday, Western and African diplomats called for an urgent deployment of peacekeepers to Somalia as al-Qaeda's deputy leader urged an Iraq-style fight against Ethiopian forces there.
Diplomats fear the Islamic courts, easily out-gunned in conventional warfare, may resort to guerrilla tactics.
Thursday's message from Ayman al-Zawahri, deputy to Osama bin Laden, posted on a website used by militant Islamist groups, is likely to reinforce Washington's belief that the Somalia Islamic Courts Council is linked to and even run by an al-Qaeda cell, a charge that UIC officials have denied.
Saeed Jenait, head of the Peace and Security Committee of the African Union (AU) in Ethiopia, told Al Jazeera that the union was studying ways of funding a peacekeeping force in Somalia and that a decision would be taken in the next few days.
"We are talking about sending 8,000 peacekeepers, but the situation in Somalia must be reassessed," he said.
"We might call for countries from the region to participate. The AU peacekeeping force will be sent in days."
|"The AU peacekeeping force will be sent in days."|
Saeed Jenait, head of the Peace and Security Committee of the African Union
Meeting in Nairobi, the International Contact Group on Somalia, which includes the US, European and African nations, met Abdullahi Yusuf, the Somali president, and also pushed for a fast deployment of peacekeepers.
Jendayi Frazer, the US assistant secretary of state for African affairs, said the security vacuum left after the defeat of the UIC needed to be filled. But she downplayed the al-Qaeda call to arms.
"I think a lot of bold statements were made by extremists in the Courts, that they were going to kill Somalis, that they were going to stand and fight... And they just ran," Frazer told Reuters after the meeting.
The Somali government wants a foreign peacekeeping force, approved by the United Nations before the war, to be deployed.
Uganda said it was ready to send troops to Somalia as soon as its parliament approves the plan, a move welcomed by the Contact Group on Friday.
Within hours of the UIC leaving Mogadishu, militiamen loyal to faction commanders ousted in June reappeared at checkpoints in the city where they used to rob and terrorise civilians.
Kenya's closure of its border crossing points has left hundreds fleeing fighting unable to cross over and seek refuge at camps, aid workers say.
A local police chief said several suspected fighters were arrested and some had been taken to Nairobi for questioning.
The US has deployed warships off the Somali coast to hunt fleeing Courts fighters.
"As far as chasing down the terrorists goes, I think they are cornered and we will see what happens," Frazer said.