Gates, along with Eric Holder, the US attorney general, has been tasked with carrying out a review to determine the fate of detainees held in the US facilities.
Barack Obama, the US president, was widely praised for moving to shut down the US prison at Guantanamo Bay, Cuba, within days of his inauguration last month.
But with his move to send 17,000 troops to Afghanistan to shore up US operations there, the Bagram prison looks set to become more visible and controversial.
Rumi Nielson-Green, a spokeswoman for the US military, told Al Jazeera that the detainees held at Bagram were "unlawful enemy combatants".
"They are individuals who have been removed from the battlefield because they are dangerous to our forces or our coalition partners," she said.
Basic rights urged
Amnesty International has urged Obama to continue its break from his predecessor's "unlawful detention policies" by ensuring that "all US detentions in Afghanistan comply with international law" and giving the detainees access to US courts.
"Judicial review is a basic safeguard against executive abuse and a protection against arbitrary and secret detention, torture and other ill-treatment and unlawful transfers from one country or government to another," the human rights group said.
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- US accused of extraordinary rendition - sending suspects to foreign countries for torture and interrogation
- Suspects sent to secret prisons have no rights under US law
- Poland and Romania reported to host secret CIA jails between 2003 and 2005
- Rights activists claim "black sites" existed in Morocco, Djibouti and Thailand
- President Obama has ordered a review of detention practices
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"In the absence of judicial oversight, detainees in Bagram, as at Guantanamo, have been subjected to just such abuses - even children have not been spared."
The rights group says that most of the 615 detainees being held at Bagram without access to courts or legal counsel are Afghan nationals, and that some of them have been held for years.
While the Obama administration has committed itself to resolving the 240 or so Guantanamo cases within a year, it has not stated its intentions on Bagram.
John Bates, a US district court judge who is hearing petitions filed by four detainees held at Bagram, has given the administration until Friday to "refine" its position on the use of the air base as a detention facility.
The administration of George Bush, Obama's predecessor, had argued that as "enemy combatants", Bagram detainees had no right to challenge their detention in US courts – the same argument it made concerning detainees at Guantanamo.
But the US Supreme Court ruled last year that inmates at Guantanamo had the right to challenge their detentions in US courts, a ruling that rights groups hope will be extended to Bagram detainees.