J. Scott Applewhite / AP Photo As the CIA digs in against criminal prosecutions, Obama must decide: Does he alienate the agency or push for justice?

The pressure seems to be getting to CIA Director Leon Panetta. On Monday night, a confidential report by the International Committee of the Red Cross detailing CIA torture and detention practices during the Bush administration was published by the New York Review of Books. In an article for The Daily Beast on April 8, I wrote that Panetta’s position against the investigation and prosecution of those potentially guilty of criminal activity is compromised because a number of his top aides are implicated in the torture program. The following day, April 9, possibly in response to the growing furor, Panetta sent a letter to CIA employees, referring to the “continuing media and congressional interest in reviewing past rendition, detention, and interrogation activities that took place dating back to 2002,” including issues involving the involvement of private contractors in CIA activities.

In short, Panetta’s letter to CIA employees simply doesn’t make sense. Is he really aware of what is actually going on?

In his letter, Panetta outlines the agency’s “current policy regarding interrogation of captured terrorists,” stating: “Under the Executive Order, the CIA does not employ any of the enhanced interrogation techniques that were authorized by the Department of Justice from 2002 to 2009.” He also declares: “CIA officers do not tolerate, and will continue to promptly report, any inappropriate behavior or allegations of abuse.” He seems defensive.

Panetta also makes the following interesting statement: “CIA no longer operates detention facilities or black sites and has proposed a plan to decommission the remaining sites. I have directed our agency personnel to take charge of the decommissioning process and have further directed that the contracts for site security be promptly terminated. It is estimated that our taking over site security will result in savings of up to $4 million.”

This is a strange set of claims and it is difficult to know how to parse them. Panetta seems to be saying that “there are no sites,” that “we’ve submitted a plan to close the sites,” and that “we’re closing the sites” all at the same time. But then he also makes it sound as though the CIA is “taking charge” of the sites from contractors, and that “taking over” the sites will save $4 million, suggesting they’re being kept open for the time being. (From where comes the $4 million in savings? If the sites are being closed, isn’t the money saved anyway?) Each of his statements seems to contradict the last. At a later point in the note, Panetta writes, “CIA retains the authority to detain individuals on a short-term transitory basis.” But where is the agency going to hold them, if the sites are closed? Panetta does not explain.

In short, Panetta’s note simply doesn’t make sense. In the end, his point seems to be that the sites exist, but are not being used currently, and may be closed in the future—except that they won’t, because the CIA retains the power to detain. Is Panetta really aware of what is actually going on?

Perhaps he’s discombobulated. Panetta has increasingly been in the hot seat because of his remarks indicating that he believes no CIA personnel should be investigated for abuse if their actions relied on legal assurances from the Department of Justice—a reference to memos written during the Bush administration by the Office of Legal Counsel, which, through deeply flawed and now repudiated legal analysis, attempted to offer legal justifications for the CIA’s various torture techniques from 2002-2006. (These methods include sleep deprivation, forced standing, and prolonged isolation—methods used by the Soviets and North Koreans—to outright physical assaults, binding or confining prisoners into painful positions, and waterboarding.)

Panetta reiterated the claim on Wednesday in his letter to CIA employees, writing, “Officers who act on guidance from the Department of Justice—or acted on such guidance previously—should not be investigated, let alone punished. This is what fairness and wisdom require.”

But as I discussed in my Daily Beast article, Panetta’s arguments about “legal reliance” are misplaced and inaccurate as a matter of criminal law. And as a general matter, it increasingly appears as though he’s more interested in protecting various CIA officials beneath him—holdovers from the Bush era—than in cleaning up the CIA.

It is important to note, however, that “cleaning up the CIA” doesn’t mean a purge. The agency has thousands of officers and directors, and only a few are implicated in the past crimes. In any case, many of the most tainted directors have already left.

Moreover, investigations of existing staff shouldn’t focus on lower-level officers. Accountability, if it ever occurs, should focus primarily on executive-level directors, such as the current CIA Deputy Director Stephen Kappes and Michael Sulick, the director of the CIA’s National Clandestine Service—both high-level officials in the CIA’s operations directorate when the worst detainee abuses were committed.

Investigations should focus also on high-level executive officers in the CIA’s Counterterrorism Center (CTC) who are still at the agency, for example, G— —, a former deputy to Jose Rodriquez, the chief of CTC back in 2002-2004 and who now enjoys a prestigious CIA station-chief posting in Europe. (I can’t reveal her name or posting; it remains covert. It should also be noted that the former CTC chief of operations also remains at the agency.)

Yet it is inappropriate to place this whole mess on Panetta’s shoulders. Attorney General Eric Holder is also a central actor in these matters. It is the Department of Justice’s responsibility to investigate and, if possible, prosecute alleged cases of torture and other violations of criminal law. Members of Congress, too—especially senior leaders on the Senate and House intelligence committees—have an obligation to insist on accountability from the administration.

Ultimately, of course, the failure of the Obama administration to address the Bush administration’s crimes lies with President Obama. So far, he is sending the wrong message to both the CIA and the Department of Justice. And yet the furor continues to grow. President Obama will only lose more credibility if he tries to ignore it.

John Sifton is a private investigator and attorney based in New York City. His firm, One World Research, carries out research for law firms and human-rights groups, including in South Asia, the Middle East and North Africa. He has conducted extensive investigations into the CIA interrogation and detention program.