Concerns over missed red flags in Navy Yard shooter Aaron Alexis’s background have thrust the federal government’s security clearance program into the spotlight.

That intensified last week when it was revealed that the same company, USIS, that performed a background investigation of National Security Agency leaker Edward Snowden had also performed Alexis’ check in 2007.

Lawmakers have demanded an investigation.

But the problem is likely bigger than one company. The Office of Personnel Management, which along with its contractors account for 90 percent of the federal government’s background investigations, has faced persistent challenges with security clearances over the years, according to the Government Accountability Office.

“A recurring theme is quality,” said Brenda Farrell, director of defense capabilities and management issues at GAO, in an interview on Federal Drive with Tom Temin and Emily Kopp.

Since the 1990s, GAO has called on the government to account for quality and metrics in the security clearance process to achieve better outcomes, Farrell said. “And one of the positive outcomes we noted was maximizing the likelihood that individuals who are security risks will be scrutinized more closely.”

Quality a victim of speedier processing?

Ten years ago, complaints about the security-clearance process centered on a different issue: timeliness. At the time, OPM struggled under a backlog of open investigations totaling more than 350,000 cases. The 2004 Intelligence Reform and Terrorism Prevention Act mandated OPM complete background investigations in 60 days.

OPM met that goal, for which it has received praise. GAO even removed security clearances from its High Risk List, which tallies up federal programs at risk for waste and fraud.

But other best practices remain elusive.

“Quality is not something that has been a priority,” Farrell said. “There was not a focus, and has not been a focus, on quality even though GAO, as I said, has been noting this is something that desperately needs attention since the 1990s.”

For example, in a 2009 report, GAO reopened about 3,500 background investigations conducted by OPM and found 87 percent of them were missing proper documentation.

Other agencies have raised concerns about the quality of the background investigations that they receive from OPM, Farrell said. “So, I don’t think that this is a little-known secret; it’s a challenge of how do you build that quality in.”

Even more fundamental questions about the process, such as official guidance about what types of positions should require what types of clearances — known as requirements determination — remain in limbo.

“We know from step one — determining whether a position needs to have a person hold a clearance — there are not guidelines in place to help agencies make that decision. And that’s very key, because depending upon the type of position a person holds, that’s when you determine what type of background investigation they need.”

Currently, about 4.9 million federal employees and contractors hold security clearances. However, according to a GAO report from June 2012, the director of national intelligence (DNI) has failed to provide agencies with clear guidelines about which positions require clearances.

“That hasn’t been done,” Farrell said. “We don’t know if 5 million people need to have clearances in the first place.”

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