Navy SEAL William “Ryan” Owens was killed in the raid on a branch of al-Qaeda, also known as AQAP, in al-Bayda province, which the Pentagon said also killed 14 militants.
However, medics at the scene said about 30 people, including 10 women and children, were killed.
US Central Command said in a statement that an investigating team had “concluded regrettably that civilian non-combatants were likely killed” during Sunday’s raid. It said that children may have been among the casualties.
It said its assessment “seeks to determine if there were any still-undetected civilian casualties in the ferocious firefight”.
US military officials told Reuters that Mr Trump approved his first covert counter-terrorism operation without sufficient intelligence, ground support or adequate backup preparations.
As a result, the three officials said, the attacking SEAL team found itself dropping onto a reinforced al-Qaeda base defended by landmines, snipers, and a larger than expected contingent of heavily armed Islamist extremists.
The Pentagon directed queries about the officials’ characterisation of the raid to US Central Command, which pointed only to its statement on Wednesday.
“Centcom asks for operations we believe have a good chance for success and when we ask for authorisation we certainly believe there is a chance of successful operations based on our planning,” Colonel John Thomas, US Central Command spokesman, said.
“Any operation where you are going to put operators on the ground has inherent risks.”
The US officials said the extremists’ base had been identified as a target before the Obama administration left office on 20 January, but then-President Barack Obama held off approving a raid ahead of his departure.
A White House official said the operation was thoroughly vetted by the previous administration and that the previous defence secretary had signed off on it in January. The raid was delayed for operational reasons, the White House official said.
The military officials who spoke to Reuters on condition of anonymity said “a brutal firefight” killed Mr Owens and at least 15 Yemeni women and children. One of the dead was the eight-year-old daughter of Anwar al-Awlaki, a militant killed by a 2011 US drone strike. Nawar al-Awlaki was a US citizen.
An unnamed official said: “Almost everything went wrong.”
Some of the women were firing at the US force, Pentagon spokesman Captain Jeff Davis told reporters.
The American elite forces did not seize any militants or take any prisoners offsite, but White House spokesman Sean Spicer said on Wednesday the raid yielded benefits.
“Knowing that we killed an estimated 14 AQAP members and that we gathered an unbelievable amount of intelligence that will prevent the potential deaths or attacks on American soil – is something that I think most service members understand, that that’s why they joined the service,” he said.
A senior leader in Yemen’s al-Qaeda branch, Abdul Raouf al-Dhahab, and other militants were killed in the gun battle, al-Qaeda said.
One of the three US officials said on-the-ground surveillance of the compound was “minimal, at best”.
“The decision was made ... to leave it to the incoming administration, partly in the hope that more and better intelligence could be collected,” that official said.
As Sunday’s operation intensified, the raiders called in Marine helicopter gunships and Harrier jump jets, and then two MV-22 Osprey vertical takeoff and landing aircraft to extract the SEALs.
One of the two Ospreys suffered engine failure, two of the officials said, and hit the ground so hard that two crew members were injured, and one of the Marine jets had to launch a precision-guided bomb to destroy it.
Mr Trump travelled to Dover Air Force Base in Delaware on Wednesday in an unexpected visit to meet the family of Owens, who had been a chief special warfare operator.
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