Brigadier General Stephen Clark from US Central Command headquarters in Florida has been named to probe the last weekend's incident which has triggered a fury in Pakistan.
Announcing the appointment of the high-level probe, US Central Command (CENTCOM) Commander General James Mattis said the Governments of Afghanistan and Pakistan would be invited to participate into the investigation.
The investigation team has also been directed to include input and participation from NATO-led International Assistance Security Force (ISAF) in Afghanistan.
US Central Command, which oversees US forces in the Middle East and Afghanistan, said in a statement that the governments of Pakistan and Afghanistan had been asked to join the probe to determine "what happened and preclude it from happening again."
Clark, posted at Headquarters Air Force Special Operations Command at Hurlburt Field in Florida, has been asked to provide an initial report by December 23.
The NATO-led ISAF sent an initial assessment team over the weekend to the border to look into the incident.
Pakistan has charged that the air strike was unprovoked, while Afghan and Western officials say that Pakistani forces opened fire first.
"The investigation team will focus their efforts on the facts of the incident and any matters that facilitate a better understanding of the circumstances surrounding the deaths and injuries of the Pakistan forces," the statement said.
Earlier in the day, Pentagon Press Secretary George Little said the Department of Defence has been working very hard for some time to address areas of disagreement with the Pakistanis.
"We understand there are deep concerns over the incident this weekend and we'll continue to try to engage closely with our Pakistani counterparts," Little told reporters during an off camera news briefing earlier in the day.