The warlord alleged to have overseen the killings, Gen Dostum, was a US ally
The US president says he is examining an alleged massacre in Afghanistan amid allegations the Bush administration resisted efforts to investigate it.
Barack Obama told CNN he had told officials to "collect the facts for me" and could order a full inquiry.
The allegations concern the deaths of hundreds or even thousands of Taliban fighters who had surrendered to the US-backed Northern Alliance in late 2001.
They were in the custody of a US-backed warlord, Gen Abdul Rashid Dostum.
The allegations that the prisoners were deliberately left to suffocate in shipping containers, or were shot dead through the container walls, first surfaced in 2002 but there has been no formal investigation.
On Friday the New York Times quoted government officials and human rights organisations as saying that "Bush administration officials had repeatedly discouraged efforts to investigate the episode".
The issue has gained fresh urgency since Gen Dostum was reinstated as military chief of staff to the Afghan president last month.
At present he remains in exile in Turkey after being suspended last year over allegations he threatened a political rival at gunpoint.
'We have to know'
Now Mr Obama says he is looking into the affair.
Alleged atrocity occurred as Gen Dostum took charge of some 4,000 prisoners amid a mass Taliban surrender in late November 2001
Prisoners were being transported from Kunduz to Sheberghan prison, west of Mazar-e-Sharif
Allegations of massacre heard by two investigators from Physicians for Human Rights, who visited prison at Sheberghan in January 2002; investigators later uncovered apparent mass grave at Dasht-e Leili
Newsweek reports deaths occurred from suffocation among prisoners packed one on top of another in the containers; testimony gathered by New York Times suggests prisoners were also fired on and killed while inside containers
Alleged survivors told Newsweek they were so desperate with thirst that they licked perspiration from each other's bodies
"The indications that this had not been properly investigated just recently was brought to my attention," Mr Obama told CNN in an interview to be aired at 2200 on Monday (0200 Tuesday GMT).
"So what I've asked my national security team to do is to collect the facts for me that are known, and we'll probably make a decision in terms of how to approach it once we have all of the facts gathered up," he said, according to excerpts released in advance.
On the question of whether he could order a full investigation, he replied: "I think that there are responsibilities that all nations have, even in war.
"And if it appears that our conduct in some way supported violations of laws of war, then I think that we have to know about that."
According to Newsweek and New York Times reports published in 2002, the prisoners died in crowded container trucks while being transported from Kunduz in northern Afghanistan to Sheberghan prison, west of Mazar-e-Sharif.
The prisoners were allegedly left to suffocate to death, or were shot inside the containers, before being buried in mass graves.
The estimates of the number who died range from several hundred to 2,000.
A mass grave has been found near the site of the alleged killings
At the time Gen Dostum was on the CIA payroll and his militia was working closely with US forces, the New York Times said.
It said the US government was also worried about destabilising the government of Hamid Karzai, in which Gen Dostum was serving as a defence official.
The newspaper quoted Pierre Prosper - who served as the envoy for war crimes under President George W Bush - as saying that, at the White House, "Nobody said no to an investigation, but nobody ever said yes, either.
"The first reaction of everybody there was, 'Oh, this is a sensitive issue; this is a touchy issue politically.'"
Gen Dostum has admitted that up to 200 prisoners died in containers while being transported to prison, but insists their deaths were unintentional.