"Almost everything went wrong", a US defense official told NBC News after the operation.
USA drones also launched six strikes on Al Qaeda strongholds in Al Sowmaa district of Bayda, the province where United States navy Seals carried out a raid in January.
The airstrikes Thursday in areas under AQAP's control marked the first USA combat action in Yemen's civil war since the January 29 raid and were coordinated with Yemen's nominal president, Abdrabbuh Mansur Hadi, according to the Pentagon statement by Navy Capt. Jeff Davis, a spokesman.
The Yemen raid was planned on January 25 at a dinner meeting attended by Trump, Vice President Mike Pence, Chief Strategist Steve Bannon, Trump's son-in-law Jared Kushner and key security advisers.
However, the SEAL's father, William Owens, has demanded a broader investigation into what he told the Miami Herald was a "stupid" mission.
The group has recently exploited the chaos of Yemen's civil war, which pits Shiite Houthi rebels and allied army units against a Saudi-led coalition battling to restore the internationally recognized government.
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Four suspected militants who had been standing outside the house were killed, he said. Local reports in Yemen have said as many as 25 civilians may have been killed during the raid.
Another strike targeted the jihadists in the Sawmaa district of the province, the local official said.
However, deaths were reported only from Shabwa, where United States drones struck Al Qaeda targets in Al Saeed district, according to a journalist in the province. They said US airstrikes targeted al-Qaeda artillery and other sites, and that no US Navy ships participated in the mission. There were no immediate reports of casualties.
They said they heard loud explosions early this morning in Al-Maraqisha, a rugged mountainous area where Al-Qaeda militants took refuge past year after they were driven out of Yemeni cities they had captured earlier.
As many as 16 civilians - eight women and eight children - were also killed in the strike, a provincial official said, drawing condemnation from human rights groups.
O'Brien expressed anger at being prevented on Tuesday from visiting the flashpoint southwestern city of Taez.