The investigation comes as the Pentagon said Thursday that the fourth soldier, Sgt. La David Johnson, was "separated" from his fellow soldiers but never left behind.
"We don't leave anyone behind.... He was separated," chief Pentagon spokesperson Dana White said of Johnson, whose body wasn't recovered until more than 24 hours after the Oct. 4 firefight.
Joint Staff Director Lt. Gen. Kenneth McKenzie told reporters during a Pentagon briefing that U.S., French and Nigerien forces never left the battlespace until Johnson's body was found by local Nigerien soldiers.
Until today, U.S. Africa Command had been conducting an informal review to gather facts about the ambush, but two weeks later, the details of the deadly incident remain unclear.
On Thursday night, a U.S. official said that the FBI would assist the military in its investigation.
Since the attack, U.S. Africa Command has been gathering facts about the ambush and the circumstances that led to it, but now a general officer will lead the new investigation.
In addition to gathering details about the incident, the larger investigation could make recommendations about how to prevent similar attacks from occurring in the future.
Many questions remain about the deadly ambush.
Were the American and Nigerien soldiers too exposed to a potential attack? Why did it take so long to locate the American soldier who was missing following the attack? Why was there was no overhead surveillance above the unit's visit to a remote village along the border with Mali?
Meeting with the Israeli defense minister at the Pentagon, Secretary of Defense James Mattis was asked if the Niger ambush was a U.S. intelligence failure and what more could have been done to save lives. He went on to speak about the deadly incident for more than five minutes.
“One comment, having seen news reports, the U.S. military does not leave its troops behind and I’d just ask not question the action of the troops that were put in the firefight and question," Mattis said. "Don't question if they did everything they could in order to bring everyone else out at once and don’t confuse your need for accurate information with our ability to provide it immediately in a situation like this."
Mattis did clarify that French armed fighter aircraft, armed helicopter gunships and a medevac helicopter responded to the scene, evacuating the wounded Americans. A U.S.-contracted aircraft evacuated the dead, he said.
There are 800 American military personnel in Niger, most in support of a drone surveillance mission for West Africa that operates from Niger's capital of Niamey. The mission is designed to help West African countries counter various Islamic extremist groups that operate in the region.
The bulk of the American forces are involved in the construction of a second drone base in Niger's northern desert region.
A smaller part of the U.S. military mission in Niger involves U.S. Army Special Forces "Green Berets," who advise and assist Niger's ground forces in combating the extremist groups.
The American and Nigerien troops that were ambushed two weeks ago were on a joint mission to meet with leaders in a village located on Niger's border with Mali.
U.S. officials have provided varying accounts of what happened on Oct. 4 and said there is still a lot of confusion about the incident.
An initial narrative described a team of about 12 soldiers from a Green Beret unit accompanying 40 Nigerien soldiers to meet with locals at a village close to Niger’s border with Mali. They were ambushed by 50 fighters believed to be from ISIS in the Greater Sahara.
A more recent narrative indicates it was a small team of eight to 12 American and Nigerien forces who came under attack during the mission to the village. The Nigerien platoon was nearby but was not a part of the mission to the village nor was it involved in the firefight. Pentagon officials have said Army Special Forces have carried out 29 previous missions like this one over the past six months without encountering any problems.
ABC News' Mike Levine contributed to this report.