The New York Times reported on Friday that two Afghan prisoners held at Bagram were tortured to death by American soldiers in 2002, according to the leaked file.
The file found the deaths were not isolated cases, as had been previously reported, but were part of a wider pattern of abuse.
Seven soldiers have been charged, including four last week, but no one has been convicted in either death.
Dilawar, a 22-year-old Afghan taxi driver detained on suspicion of involvement in a rocket attack on a US military base in the south-eastern province of Khost received over 100 blows to the legs.
By the time Dilawar underwent his final investigations, interrogators believed he was innocent, the report added.
Habibullah died of a heart attack six days earlier. The report said it was likely to have been caused by a blood clot produced by repeated blows to the legs.
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.
In sworn statements soldiers described a female interrogator stepping on the neck of one prostrate detainee and kicking another in the genitals, and another shackled prisoner was forced to kiss the boots of his interrogators.
Last October the investigation concluded there was cause to charge 27 personnel in the Dilawar case with dereliction of duty, maiming and involuntary manslaughter.
Fifteen of the same soldiers were cited for probable responsibility in the Habibullah case, the New York Times reported.
A Whitehouse spokesman confirmed an investigation was underway.
“There are criminal investigations going on right now about what this newspaper article discusses,” spokesman Trent Duffy told reporters.
Asked about the report, President George W. Bush said: “I’m comfortable that we’re getting to the bottom of the situation and I know we’re doing so in a transparent way.
“Obviously, ours is a country that respects human rights and human dignity, and if those rights and dignity have been denied, we will hold people to account,” the president said.
The latest allegations of prisoner abuse, as well as recent anti-US protests in Kabul sparked by an erroneous story about desecration of the Koran by US guards, threaten to overshadow a visit by Afghan President Hamid Karzai to Washington beginning on Saturday.