The announcement follows a report on Friday in The New York Times, detailing the torture of two detainees at the hands of young and badly trained US soldiers resulting in their deaths.
"Absolutely, this is being investigated thoroughly," Trent Duffy, a White House spokesman said.
Two Afghan prisoners held in a US-run prison in Bagram were tortured to death by American soldiers in 2002, the paper said, quoting a 2000-page file on the US army's criminal investigation of the case.
"There are criminal investigations going on right now about what this newspaper article discusses. People are being held to account," Duffy said.
Although the two deaths were reported earlier, the newspaper report gave a graphic account of their abuse. The report comes at a sensitive time in Afghanistan after at least 14 people were killed in anti-US demonstrations sparked by reported desecration of the Quran by US investigators at Guantanamo Bay.
Bagram near Kabul serves as the
main US base in Afghanistan
The 2000-page file on incidents at the Bagram detention centre near Kabul shows repeated incidents of maltreatment.
"Sometimes the torment seems to have been driven by little more than boredom, cruelty, or both," the report said.
Dilawar, a 22-year-old Afghan taxi driver detained on suspicion of involvement in a rocket attack on a US military base in the southeastern province of Khost received more than 100 blows to the legs and an autopsy found that the tissue in his legs had been pulverised.
"I have seen similar injuries in an individual run over by a bus," Lieutenant Colonel Elizabeth Rouse, a coroner and a major at the time, said in the classified US report, the daily said.
By the time Dilawar underwent his final investigations, interrogators believed he was innocent, the report added.
Induced heart attack
Another Afghan, Habibullah, died of a heart attack, which the report said was likely to have been caused by a blood clot produced by repeated blows to the legs.
An investigation into abuse of detainees in US military custody in Afghanistan conducted by General Charles Jacobi in 2004 remains classified, although US military spokesmen insist prisoners at Bagram, the main US detention facility in Afghanistan, are now being treated humanely.
Anti-US sentiments are running
high in Afghanistan
The former commander of US forces in Afghanistan Lieutenant-General David Barno earlier said the two deaths were isolated cases, although eight prisoners are known to have died in US custody.
However, the army criminal investigation report tells a different story, despite the fact many of the officers and soldiers interviewed in the Dilawar investigation said the large majority of detainees at Bagram were compliant and reasonably well treated.
In sworn statements to US army investigators, soldiers describe one female interrogator with a taste for humiliation stepping on the neck of one prostrate detainee and kicking another in the genitals, The New York Times reported.
Another shackled prisoner was forced to roll back and forth on the floor of a cell, kissing the boots of his two interrogators as he went.
Yet another prisoner was made to pick plastic bottle caps out of a drum mixed with excrement and water as part of a strategy to soften him up for questioning, the paper reported.