The investigation was ordered on Wednesday after e-mail messages sent in by FBI agents describing the abuse of inmates at the secretive detention centre became public last month.
Two officers have been tasked by the military's Southern Command, which has jurisdiction over Guantanamo Bay, to investigate the abuse allegations.
The FBI e-mail messages described Guantanamo prisoners being shackled hand and foot in a foetal position on the floor for 18 to 24 hours, and left to urinate and defecate on themselves.
One FBI agent reported seeing a barely conscious prisoner who had torn out his hair after being left overnight in a sweltering room.
Another told of an interrogation in which a prisoner was wrapped in an Israeli flag and bombarded with loud music and strobe lights.
SouthCom officials said an army general and a navy captain would travel to Guantanamo this week to begin investigating the allegations.
They have been ordered to report back to SouthCom commander General Bantz Craddock by 1 February.
But it was likely the deadline would be extended to allow the two officials to interview personnel no longer working at Guantanamo.
"It is specifically going to concentrate on those allegations raised by the FBI e-mails and memoranda but it's not limited to that," SouthCom spokesman Raul Duany said.
The e-mail messages were written by FBI agents who had worked at Guantanamo and were made public by the American Civil Liberties Union which obtained them under the Freedom of Information Act.
The United States has been holding about 500 terror-suspects at Guantanamo, most of them captured during the invasion of Afghanistan in 2001.
US troops have been accused of abusing prisoners in Iraq and Afghanistan.