The Pentagon said the 15-strong group will fly to Bagram air base near Kabul to begin its mission within the next 48 hours.
The US has acknowledged that there were civilian deaths when an AC-130 attack aircraft raided villages in the province of Uruzgan in central Afghanistan last week, but it maintains its pilots were responding to anti-aircraft fire.
Afghan officials say 48 civilians died and 117 people were wounded in the strikes, including guests at a wedding in the village of Dehrawad, 400 kilometres (250 miles) south-west of Kabul.
The investigative team will be led by an Air Force general and include experts in air traffic control and AC-130 attack aircraft.
The probe follows a preliminary investigation last week in which US officials visited Dehrawad and talked to villagers about what happened.
Toll uncertain
Pentagon spokeswoman Victoria Clarke said the US regretted "every one" of the civilians casualties of the attack, but said the US did not have "hard and fast numbers" of victims.
"The team will take as long as they need to tour the sites, interview villagers, pilots, forward air controllers and special forces and to do as thorough as possible a job on the investigation," she said.
She said Washington had asked Afghan leader Hamid Karzai to appoint an Afghan to join the team.
Despite the continuing controversy over the incident, US defence officials will not rule out future air strikes.
"We intend to use whatever tools and tactics we think are appropriate at different times," said Ms Clarke.
Taleban 'in area'
The Pentagon says Uruzgan province had been under surveillance since February, and there was intelligence that there might have been several high-level leaders of the former Taleban regime in the area.
The director of operations for the US Joint Chiefs of Staff, Lieutenant General Gregory Newbold, insisted that US-led forces operating in the area had come under attack.
"I don't think there's any question that our aircraft and our forces on the ground were fired at, so, the investigation will determine the detail of what specifically precipitated the strike," he said.
The Pentagon said the US plans to increase the number of troops in Uruzgan province to help relief operations there but would not expand its mission to include peacekeeping in Afghanistan.
It comes amid calls for the US to beef up the International Security Assistance Force (Isaf) in Afghanistan following the assassination of Afghan Vice-President Haji Abdul Qadir in Kabul on Saturday.