On January 22, 2009, Barack Obama signed an executive order that closed all CIA-operated black sites. The text of the order was carefully drawn, and the shutdown was limited to the CIA. If black sites were being run by other agencies, they were left standing, though other aspects of the order that would have applied to them addressed abuses of the Bush era. Since then, it is increasingly obvious that Secretary Gates’s Department of Defense is operating a two-tiered detentions system in Afghanistan. One tier is openly touted as the essence of the new, Obama-era detentions. The other is kept in the shadows. Now the BBC’s Hilary Andersson joins the New York Times and Washington Post in reporting on the secret detentions regime:

Nine former prisoners have told the BBC that they were held in a separate building, and subjected to abuse. The US military says the main prison, now called the Detention Facility in Parwan, is the only detention facility on the base. However, it has said it will look into the abuse allegations made to the BBC. The International Committee of the Red Cross (ICRC) said that since August 2009 US authorities have been notifying it of names of detained people in a separate structure at Bagram. “The ICRC is being notified by the US authorities of detained people within 14 days of their arrest,” a Red Cross spokesman said. “This has been routine practice since August 2009 and is a development welcomed by the ICRC.” The spokesman was responding to a question from the BBC about the existence of the facility, referred to by many former prisoners as the Tor Jail, which translates as “black jail”.

The BBC adds that “Vice Adm Robert Harward, in charge of US detentions in Afghanistan, denied the existence of such a facility or abuses.”

My bet is that Admiral Harward, who is usually cautious in his wording, denied that any such facility existed under his command. That distinction would be critical, because the available evidence points to this detention operation and several others, being conducted under the authority of the U.S. Joint Special Operations Command or JSOC, which often operates in Afghanistan outside of General McChrystal’s command.

This raises questions that should be put to Secretary Gates forcefully. Why is JSOC being allowed to run a self-standing detentions operation? (JSOC will no doubt deny that it is a detentions operation, putting its activities within its core intelligence-gathering mission, but that doesn’t change the facts.) Why is JSOC being allowed to operate a facility applying its own rules, including the use of impermissible techniques such as hypothermia and long-term sleep deprivation? Why was the Red Cross denied access to the prison for many months following the president’s January 22, 2009 order, which insured Red Cross access? What sort of accountability system has been put in place for this secret prison? What other secret detention facilities does JSOC run? Reports have long circulated about JSOC “filtration” operations at forward positions in Afghanistan. Of course, there is also Camp Nama in Iraq and the still unexplained Camp No in Guantánamo.

No one would deny that President Obama, starting with the prohibition on torture, has cleaned up many of the worst abuses that his predecessor put in place. But it’s impossible to reconcile the current operations with the promises that candidate Obama made on the campaign trail. The secret detentions regime run by JSOC is linked with the most serious recurrent reports of abuse emerging from Afghanistan. It should now be the major focus of concern for those looking at detainee treatment issues. The JSOC black jail has been allowed to operate in the shadows for too long.