"A thorough review of intelligence and surveillance supports initial reports that all killed in the strikes were legitimate enemy targets," the statement said.
"In addition, we are working closely with Afghan partners to investigate unconfirmed reports of civilians among Mustafa's party."
Ikramudin Rezazada, the Ghor deputy governor, said Mustafa's six-year-old son was among 10 civilians killed.
"Five were children and five were adults," he said, citing local police.
"We can confirm now that Mustafa has not been killed and he has managed to flee with three of his men."
Rezazada said Mustafa has links with the Taliban and is accused of being behind a string of attacks.
According to the US military, Mustafa commands about 100 fighters and has links to the Quds force of Iran's Revolutionary Guards, which the US accuses of training Taliban fighters in Afghanistan.
The US said its forces had observed Mustafa moving by vehicle from his compound on Tuesday and launched the air attack when he and a number of his men stopped in a remote, unpopulated area.
The US military is under pressure over the number of civilians being killed and wounded in its attacks.
Afghan officials said more than 140 civilians were killed in an air raid in the Farah province in western Afghanistan last month.