Officials have again insisted that they believe the aircraft came under fire during the incident on 1 July.
But at an earlier news conference, a senior Pentagon official appeared to cast doubt on whether the aircraft had been fired on.
The Afghan Government says that 48 people were killed and 117 wounded when the Americans mistook celebratory rifle fire at a wedding party for enemy action.
The Pentagon's deputy chief of operations, Brigadier-General John Rosa, appeared to alter the US version of events surrounding the incident.
Firing 'in area'
He said that there had been firing against US ground forces in the area, but he could not be sure that any firing had been directed at US aircraft.
"I can't say unequivocally that the AC-130 was fired on. That will come out, hopefully, in the investigation," General Rosa said.
"I have seen nothing to say the aircraft was fired on. I don't know that. It could well have been," he added.
A few hours later, the Pentagon took the unusual step of issuing what it called a clarification.
It said its version of events had not changed but that the whole incident was the subject of an investigation.
US errors
The Pentagon says that, according to reports from US forces, the AC-130 gunship had come under anti-aircraft fire.
"Personnel aboard the AC-130 also reported surface-to-air fire directed at them," the statement said.
"US ground forces also witnessed fire being directed at US aircraft during the operation.".
The BBC's Pentagon correspondent, Nick Childs, has said there is no official account for why General Rosa's words appeared at odds with this version.
Sources suggested that he had only just come back from leave and had not been fully briefed.
But our correspondent says this apparent confusion is unlikely to improve the atmosphere surrounding the affair.
Relations between Washington and Kabul became strained after the incident in central Uruzgan province.
Inquiry starts
US Air Force Brigadier General Anthony Przybyslawski has arrived in Afghanistan to lead an investigation into the incident.
US Deputy Defense Secretary Paul Wolfowitz, who was in Afghanistan on Monday as part of a regional tour, said American forces always tried to avoid civilian casualties but there could be no guarantees.
He said: "We very much regret any time that innocent people are killed. All the evidence suggested that innocent people were killed (in Uruzgan)."