It was reported in the US on Friday that top officials from the previous administration of president George W Bush discouraged separate probes by US officials.
According to the reports, the move was an attempt to hush up the killing of up to 2,000 prisoners in 2001 because it was carried out by General Abdul Rashid Dostam, an Afghan warlord then on the CIA's payroll.
'The indications that this had not been properly investigated, just recently was brought to my attention,' Mr Obama said during his visit to Ghana over the weekend.
'We'll probably make a decision in terms of how to approach it once we have all of the facts gathered up,' he said.
A powerful commander in control of a section of northern Afghanistan, General Dostam first allied with the Soviets during their invasion of the country in the 1980s.
But later he sided with the US and received military and CIA support after the US invaded Afghanistan in the wake of the 11 September 2001 attacks.
The killings took place in late November 2001, shortly after the invasion that ousted Kabul's Taliban government.
Taliban prisoners captured by General Dostam's forces after a major battle in northeastern Kunduz province were allegedly packed into shipping containers and left to suffocate, or were shot through the container walls, before being buried in mass graves.
Estimates on the number of people killed have ranged from several hundred to several thousand.
