WASHINGTON (AP) -- The government's sprawling system of background checks and security clearances is so unreliable it's virtually impossible to adequately investigate the nearly 5 million Americans who have them and make sure they can be trusted with access to military and sensitive civilian buildings, an Associated Press review found. Case after case has exposed problems for years, including recent instances when workers the government approved have been implicated in mass shootings, espionage and damaging disclosures of national secrets. In the latest violence, the Navy Yard gunman passed at least two background checks and kept his military security clearance despite serious red flags about violent incidents and psychological problems. The AP's review -- based on interviews, documents and other data -- found the government overwhelmed with the task of investigating the lives of so many prospective employees and federal contractors and then periodically re-examining them. The system focuses on identifying applicants who could be blackmailed or persuaded to sell national secrets, not commit acts of violence. And it relies on incomplete databases and a network of private vetting companies that earn hundreds of millions of dollars to perform checks but whose investigators are sometimes criminally prosecuted themselves for lying about background interviews that never occurred. "It's too many people to keep track of with the resources that they have, and too many people have access to information," said Mark Riley, a Maryland lawyer who represents people who have been denied clearances or had them revoked. The Pentagon knows there are problems. Defense Secretary Chuck Hagel has ordered a sweeping review of all military security and employee screening programs. "Something went wrong," he said. Separately, Congress has asked the inspector general at the U.S. Office of Personnel Management to investigate how a clearance was awarded to Aaron Alexis, the Navy IT contractor who killed 12 people Monday inside a Washington Navy Yard building before he was shot to death by authorities. Just weeks ago, the Navy had warned employees under its new "insider threat" program that all personnel were responsible for reporting suspicious activity that could lead to terrorism, espionage or "kinetic actions" -- a military euphemism for violence. "The clearance piece of this is one, I think, we very clearly have to take another look at," said Gen. Martin Dempsey, chairman of the Joint Chiefs of Staff. The Navy Yard itself reopened for normal operations on Thursday, but it was hardly business as usual. Returning employees said they felt unsettled. Workers who streamed by the red brick wall of the Navy Yard in the early morning sun said it was too soon to talk about the week's violence. FBI Director James Comey said investigators were still working through video evidence, but fresh details of the shootings were emerging. Comey said Alexis entered the Navy Yard in a vehicle, parked in a deck across from Building 197, entered carrying a bag, went into a fourth-floor bathroom and came out carrying a Remington 870 shotgun. The shotgun was cut down at both ends -- the stock sawed off and the barrel sawed off a bit -- and ammunition was stowed in a cargo pocket on the outside of his pants. Almost immediately Alexis started to shoot people on the fourth floor with no discernible pattern, Comey said. Alexis also went down to the lobby, shot a security guard and took the guard's handgun, continuing his shooting until he was cornered later by a team of officers and killed after a sustained gunfire exchange. Comey said there was no evidence that Alexis fired shots down into the atrium despite initial accounts from witnesses at the scene. "It appears to me that he was wandering the halls and hunting for people to shoot," he said. Alexis had worked for a Florida-based IT consulting firm called The Experts. He had been refreshing Pentagon computer systems, holding a military security clearance that would have expired five years from now. The same company that investigated Alexis for his security clearance also did a 2011 follow-up investigation of Edward Snowden, the former NSA systems analyst who leaked documents about the National Security Agency. The company, USIS, said in a statement Thursday it conducted Alexis' background check in 2007 for the Office of Personnel Management but that it couldn't elaborate. USIS is under a federal investigation into possible criminal violations involving its oversight of background checks, the AP reported in July. USIS dominates the background check industry, taking in $195 million in government payments last year and more than $215 million this year. Alexis' employer said it had had no personnel problems with him and two separate background checks revealed only a traffic violation. But there were trouble signs below the surface. Public records databases used in those kinds of searches can be spotty repositories of arrest records, court dockets and other information. "The only thing that the security-clearance process is intended to protect is the security of the United States," said Shlomo Katz, a government contracts lawyer who has been issued a clearance himself and is an expert on the process. "The system is not designed to protect the lives of our co-workers, and therefore I don't view it as a failure of the system." Alexis' employer -- and possibly the government -- missed how, in September 2010, Alexis' neighbor called police in Fort Worth, Texas, after she said she was nearly struck by a bullet shot from his downstairs apartment. When police confronted Alexis about the shooting, he said he was cleaning his gun when it accidentally discharged. Alexis was arrested on suspicion of discharging a firearm within city limits. The checks also missed how, six years earlier, Seattle police arrested Alexis for shooting the tires of another man's vehicle in what he later described as an angry "blackout." Police said two construction workers reported seeing a man, later identified as Alexis, walk out of the home next to their worksite, pull a gun from his waistband and fire three shots into the rear tires of their car before he walked back home. No charges were filed in either the Fort Worth or Seattle incidents. The Experts said it had most recently used a company called First Advantage of Alpharetta, Ga., to search Alexis' past for criminal involvement. A First Advantage spokeswoman said Thursday The Experts asked only for a typical employment background check that only returns information on convictions, not merely arrests. A search for any criminal history on a similar public records service, LexisNexis, also produced no arrest records. LexisNexis says it has coverage gaps for certain public records, including arrest reports for King County, Wash., and Tarrant County, Texas -- both places where Alexis had firearm run-ins. Some local governments won't sell their data, but those arrest records would still be available from municipalities individually in what can be a tedious process. Even with complete data, the databases probably would have missed a Newport, R.I., police report last month, which didn't list Alexis as a suspect in any wrongdoing but instead reported him complaining about voices wanting to harm him. He couldn't sleep, reports stated, and believed people were following him and using a microwave machine to send vibrations to his body. He called police and told them he couldn't get away from the voices. On Aug. 7, local police did alert officials at the Newport Naval Station about being called to the naval defense contractor's hotel room. But officers didn't hear from them again. In 2005, the Pentagon's security clearance investigations moved to the Office of Personnel Management, the government's human resources service. A Senate Homeland Security subcommittee said this summer that such a move decreased backlogs and led to more-timely responses for checks, but it criticized "insufficient information-sharing or reciprocity between government agencies, limited information technology capabilities and a lack of appropriate oversight over the process and those conducting investigations." The gunman's access to the Navy Yard presented another question: How Alexis could use a security credential, called a "Common Access Card," that allowed him in and out. Issued under Defense Department authorization, the card is commonly used by both military personnel and eligible contract employees, and 3.5 million were in circulation in 2008, according to government figures. Private contractors working on military bases need national security clearances to obtain access cards. Congressional officials involved in ongoing investigations about clearance problems said they were examining whether CAC credentials are awarded too easily and recipients not rechecked frequently enough. Background checks can also be undermined by fraud. Federal prosecutors in Washington in the past several years have secured convictions against 16 background investigators for falsified checks involving lying about interviews that never occurred or claiming that they had reviewed records they hadn't. In Virginia this month, a man was sentenced to eight months in prison for coaching federal job applicants and others how to beat lie detector tests. Katz, the government contracts lawyer, said he said he wouldn't have hired Alexis knowing all the information about him available now, mostly because his arrest for shooting a stranger's car tires suggest a worker who could harm fellow employees or be dangerous in the workplace. But that decision itself would be a judgment call. "To lay the blame at the foot of the security clearance apparatus and to think that by changing some security clearance laws we're going to fix the problem is ridiculous," he said. "We have to look at the whole picture of what choices have we as a society made about gun laws, what choices have we as a society made about mental health."