Crossposted at TIME

The views expressed are the author's own and not necessarily those of the Brennan Center for Justice.

People who have never worked in a classified environment might be scratching their heads over the Justice Department’s decision to close its year-long investigation into then-Secretary of State Hillary Clinton’s use of a private e-mail system to conduct government business with no prosecutions.

In an unusually detailed statement about the case, FBI Director James Comey revealed that over one hundred e-mails containing classified information were knowingly transmitted through the insecure servers, and that “it is possible that hostile actors gained access to Secretary Clinton’s personal email account.” At least 7 e-mail chains contained information classified at the highest level, Top Secret/Special Access Program, which is reserved for materials that could be expected “to cause exceptionally grave damage to national security” if disclosed without authorization. These would seem to be facts supporting a prosecution, especially since the Obama administration has been unusually aggressive in charging people for leaks large and small.

So what gives? Obviously, many Obama administration critics will believe Clinton received special treatment because she is the Democratic Party’s nominee for the Presidency, but Comey’s Republican bona fides belie the notion that this was a decision made with partisan bias. It would have been easy for him to simply submit the facts uncovered during the investigation to the Justice Department for a prosecutive decision without a recommendation from the FBI, and without public commentary regarding his opinions on whether charges were merited. In fact it could be argued that Comey’s detailed criticism of Clinton’s behavior was itself a partisan shot taken by a law enforcer who simply didn’t have the evidence to make the charges stand up in court.

I think it is far more likely that this decision was made not to protect Hillary Clinton, but to protect a broken classification system that only serves to shield the national security establishment from public accountability. Because prosecuting a weak case against a powerful figure of substantial means would undoubtedly challenge many of the myths that prop up a secrecy regime that has long failed to accomplish its sole task of protecting national security.

First, the vast majority of information that is classified, shouldn’t be. While it is easy for Comey to say there were 110 emails with classified information in Clinton’s servers, proving they were properly classified under the Executive Order is a separate matter. The Obama Justice Department learned this lesson the hard way when its attempted Espionage Act prosecution against National Security Agency official Thomas Drake fell apart after Bill Leonard, the former director of the Information Security Oversight Office (a government agency that oversees classification policy), filed documents challenging the propriety of the NSA’s classification decisions regarding key documents in the case. The Bush administration dropped an earlier espionage case involving employees of the American Israel Public Affairs Committee under similar circumstances, after the judge ruled Leonard could testify as a defense expert.

The fact that overclassification is a persistent, costly problem that harms national security and undermines public accountability is not a secret known only to insiders. Government bodies set up to evaluate the classification system first identified overclassification as a problem of “serious proportions” in 1956 (the Coolidge Committee), and drew similar conclusions in 1957 (the Wright Commission), 1959 (the Moss Subcommittee), 1970 (the Seitz Task Force), 1985 (the Stilwell Committee), 1994 (the Joint Security Commission), and 1997 (the Moynihan Commission). In 2004 the 9/11 Commission identified overclassification as a contributor to the failure to properly analyze the available intelligence. But the recommended reforms of the classification system are rarely enacted, and the number of classified documents keeps rising.

Experts have suggested that up to 90 percent of classified materials could be made public without harming our national security. Massive releases of classified material by Chelsea Manning and Edward Snowden seem to prove the point. These leaks certainly embarrassed government officials, and undoubtedly caused them some inconveniences, but they made minimal impact on national security. In fact, by increasing democratic accountability over the intelligence community, these releases arguably made the nation more secure. That the government still considers much of the material you and I can see online still properly classified only highlights the absurdity and ineffectiveness of the system.

Second, what everyone who has worked with classified information knows is that violations are common, but enforcement is entirely arbitrary. All you have to do is list some of the high-ranking officials who were accused of mishandling classified information to get an idea how often mistakes are made by people who have large staffs to assist them with the complex rules governing the handling of these materials: CIA Director John Deutch, CIA Director Leon Panetta, CIA Director David Patreaus, Attorney General Alberto Gonzales, former National Security Advisor Sandy Berger, Lt. Gen. William Boykin, and FBI Special Agent in Charge John O’Neil.

Of course these high-ranking officials rarely faced consequences more severe than misdemeanor charges, or reprimands, if any punishment was meted out at all. While lower-level government employees and contractors who leak to the press to expose government misconduct, like Jeffrey Sterling, Chelsea Manning, Shamai Leibowitz, and Edward Snowden are charged with felonies and often receive draconian sentences.

But the dozen or so people on either of these lists are just a tiny percentage of the more than 4 million government employees and contractors who handle and potentially mishandle classified information on a daily basis. Mostly sensitive information is exposed by error or negligence, and we mostly never hear about them. But intentional leaks, such as the 2009 leak of General Stanley McCrystal’s recommendation that President Obama increase the number of U.S. troops in Afghanistan, regularly appear on the front pages of national newspapers. Yet few of these unauthorized releases of national security secrets, which are clearly designed to influence policy at the risk of damaging security, are ever even investigated, much less prosecuted. The unfairness of the uneven enforcement of these laws undermines morale within the intelligence community and reduces confidence that the rules matter.

As a former FBI undercover agent, I recognize there is a need to protect some government information in order to protect ongoing security operations, and defense plans. But the classification system we have in place is not working to protect our security. It is only protecting the national security establishment from public accountability necessary to ensure they are effective and efficient as they need to be. We can only hope that the attention the Clinton email scandal has received will lead Congress and the next president to implement reforms to reduce classification and enforce the law fairly and effectively, whether you’re a whistleblower or running for high office.