The Iraqi Minister of Defence Khaled al-Obeidi said earlier that nine soldiers died in the strike on Friday.
The U.S. military is leading an international coalition that is waging an air offensive on Islamic State in Iraq and Syria, where the militant group control large swaths of territory.
Obeidi told a news conference that the strike occurred when coalition air forces were covering the advance of Iraqi ground troops near Fallujah because the Iraqi army helicopters were not able to fly due to the bad weather.
Carter said he spoke with Iraqi Prime Minister Haider al-Abadi by phone on Saturday to express his condolences over the deaths. He said it appeared a U.S. aircraft had carried out the air strike.
“That’s the information I have now,” he told reporters while on a trip to the Middle East.
“He (Abadi) and I agreed that this was an event that we both regretted and that there would be an investigation of it, but that these kinds of things happen when you’re fighting side by side.”
Carter met with Abadi this week during a brief visit to Baghdad to assess the state of the campaign against Islamic State.