The Army appointed Maj. Gen. Kenneth Dahl, an officer with Afghanistan combat experience, to lead the probe but did not provide a timeline for its completion.
The Pentagon said Dahl would not interview Bergdahl until the reintegration team clears him for this type of questioning so there was no way to determine when it could conclude.
"The primary function of this investigation, as in any other investigation, is to ascertain facts and report them to the appointing authority," the Pentagon said in statement. "These types of investigations are not uncommon and serve to establish the facts on the ground following an incident."
Dahl and his team will not be starting the probe completely from scratch but will have access to previously gathered evidence, including the 2009 investigation.
The Pentagon also asked the public to respect the time and privacy needs of Bergdahl as he finishes the military's reintegration process before being released to his parents.
"The Army's top priority remains Sgt. Bergdahl's health and reintegration," the Pentagon said. "We ask that everyone respect the time and privacy necessary to accomplish the objectives of the last phase of reintegration."
On May 31, President Obama announced that Bergdahl, who served in Afghanistan before being captured and held prisoner by the Taliban for five years, was coming home. The Obama administration secured Bergdahl's freedom in exchange for releasing five Taliban leaders from the Guantanamo Bay prison facility.
Shortly after the announcement, soldiers who served with Bergdahl in Paktika Province, Afghanistan, came forward to say he had voluntarily left his post and may have deserted, setting off a political furor over whether the administration should have made the deal with the Taliban.
The released Taliban leaders were sent to Qatar, where the deal requires them to remain for one year.