The six bodies were dicovered on Saturday after US planes and ground troops attacked a compound east of Gardez, in Paktia province, on Friday night.
Taliban leader Mullah Jilani was believed to be hiding in the compound.
"After we went there we discovered the bodies of two adults and six children under a collapsed wall," Lieutenant Colonel Bryan Hilferty said in Kabul.
He added that the cause of the wall collapse was not known.
"I don't know what caused the collapse of the wall because although we fired on the compound there were other explosions inside the compound," he said.
The US military admitted on Sunday that an air raid had killed nine children on Saturday in the neighbouring Ghazni province.
'US troops attacked'
Hilferty said the troops in the Friday night Paktia assault had come under attack.
"There was heavy machine-gun fire so we had no indication that it was a non-combatants' zone," he said.
US forces attacked the compound from the air and ground and captured nine people during the operation.
"There was heavy machine-gun fire so we had no indication that it was a non-combatants' zone"
Lt Col Bryan Hilferty
"We took nine suspected anti-coalition forces under our custody that night," he said, adding that Jilani was not among them. "I don't know if he escaped," Hilferty said.
The United Nations has called for an inquiry into the deaths of the nine children and said its findings had to be made public.
The blunder "adds to a sense of fear and insecurity" in the country, following similar killings of innocent civilians, the UN said.
UN special envoy Lakhdar Brahimi said in a statement that the protection of civilians was an "obligation" that any military had to uphold.
The US military said a commission of inquiry was being set up to probe the deaths, adding that its forces "follow stringent rules of engagement to specifically avoid this type of incident while continuing to target terrorists".