The US air strikes in Somalia failed to kill any of the three al-Qaeda suspects they targeted, a top US official says.
Mohammed allegedly trained with Osama bin Laden in Afghanistan
The three were wanted in connection with the 1998 bombing of US embassies in East Africa and a 2002 attack on Israeli targets in Kenya.
Somali officials had earlier reported that one of the men had been killed.
The US accused Somalia's routed Islamist group of harbouring the three - charges they denied. The air strikes have been strongly criticised.
The US official, who refused to be named, however said that Somalis with close ties to al-Qaeda had been killed.
Earlier, US ambassador to Kenya and Somalia Michael Ranneberger told the BBC that Fazul Abdullah Mohammed had not been killed, contradicting Wednesday's reports.
Ambassador Michael Ranneberger also strongly denied reports that a number of civilians had died in the attack.
Washington has dismissed criticism of its first overt military action in Somalia since 1994, saying it was necessary to defend the US and the international community from further al-Qaeda attacks.
Kenyan intelligence sources said on Wednesday that Mr Mohammed's wife and the wife of Saleh Ali Saleh Nabhan, also wanted by the FBI for an attack in East Africa in 2002, had been arrested in Kenya after fleeing the coastal Somali town of Ras Kamboni.
The US government is offering a $5 million reward for the capture of Mr Mohammed.
The Islamists took control of much of southern Somalia last year before being routed by Ethiopian and Somali government forces in recent weeks.
Since taking control of the capital, Mogadishu, BBC reporter Ahmed Idawaqaca says security forces have arrested about 40 Ethiopians of Oromo origin, killing one of them. Another Oromo person has been killed in Jowhar in a similar round-up.
Oromo refugees have been living in the country for the last 14 years after Oromo rebels took up arms against the Addis Ababa government.
A local Somali MP said 27 civilians had died in recent air strikes near Afmadow.
But Mr Ranneberger denied this.
"It's been troubling to see these reports about bombing and all these activities killing civilians, I can tell you categorically that no civilians were killed or injured as a result of that action," he said.
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.
Ethiopian forces have been at the forefront of the drive against Somalia's Islamists, who deny charges they had been sheltering al-Qaeda operatives.
Mr Ranneberger also said the US would support moderate Islamists participating in a Somali government of national unity, as long as they rejected violence.
"We think that all Somalis who renounce violence and extremism have a role to play in the future of the country," he said.
On Wednesday, Ethiopian Prime Minister Meles Zenawi said several terror suspects had been either killed or captured in the strikes.
He told reporters Ethiopian forces had gone to the scene of Monday's US raid and collected the dead and wounded.
He said those killed "may have involved very senior Islamist court leaders".
The UK Foreign Office is currently investigating reports that Britons are among those killed in the fighting after Somali officials said they had found a variety of international passports on the bodies of dead Islamist fighters.
The United Nations Security Council on Wednesday again backed plans to send African peacekeepers into Somalia to help protect the transitional government, enabling Ethiopian forces to withdraw.
The initiative was agreed before the Union of Islamic Courts' militia were ousted by Ethiopian-backed government forces.
The Security Council also supported sending a UN humanitarian mission to the Kenya-Somalia border.
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.