Djibouti, which hosts a large United States anti-terror base, has condemned this week's US air strikes in neighbouring Somalia.
Ethiopia was at the forefront of the drive against Islamists
Foreign Minister Mahmoud Ali Youssouf told the BBC that the raid was counterproductive to achieving peace.
He said his government had not received prior warning about the strikes, which are reported to have been launched from the US base in Djibouti on Monday.
The US says it was targeting al-Qaeda suspects but says they were not killed.
Somali's interim government has backed the air strikes, in which a US official says that Somalis linked to al-Qaeda were killed.
The government backed by Ethiopian forces has recently ousted Islamists, accused of sheltering foreign al-Qaeda operatives, from much of the country.
The Islamists deny any links to al-Qaeda.
Mr Mahmoud also said his government was very worried about reports of Somali civilian casualties and that past foreign military intervention in Somalia had not brought about the expected result.
This is presumably a reference to the last US intervention in Somalia, from 1992-94, which ended in a humiliating withdrawal following the killing of 18 US troops.
The US 1,500-strong Combined Joint Task Force - Horn of Africa was set up in Djibouti following the 9/11 attacks on the US.
The US has long said that the 1998 attacks on its East African embassies and the 2002 attacks on Israeli targets in Kenya had strong links to Somalia.
But it says the top three suspects in those attacks - Comoros national Fazul Abdullah Mohammed, Kenyan Saleh Ali Saleh Nabhan and Abu Taha al-Sudani of Sudan - all survived this week's air strikes.
Somali officials had earlier reported that Mr Mohammed had been killed.
The US government is offering a $5m reward for his capture.
US ambassador for Kenya and Somalia Michael Ranneberger has denied reports that a number of civilians had died in the attack.
Deputy Somali Prime Minister Hussein Aideed, however, told the BBC that the loss of civilian lives during the attacks was justified to stop "an alliance of the ousted Islamic Courts Union and al-Qaeda" from taking over Somalia and then going to Kenya and Ethiopia.
Residents of Afmadow town and Ras Kamboni reported further attacks on Tuesday and Wednesday but Mr Ranneberger said these had not been carried out by US forces.
Reports suggest Ethiopian MiG fighters and helicopter gunships seen in the city of Kismayo may be involved.
Aid workers report that more 1,000 people have been wounded since fighting erupted in December.
However, there is no reliable information on casualties in the current fighting in the remote south.
Correspondents say the situation on the ground in southern Somalia remains unclear, with communications in the area poor.