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 The company that conducted a background investigation on the contractor Edward J. Snowden fraudulently signed off on hundreds of thousands of incomplete security checks in recent years, the Justice Department said Wednesday. 
 
 The government said the company, U.S. Investigations Services, defrauded the government of millions of dollars by submitting more than 650,000 investigations that had not been completed. The government uses those reports to help make hiring decisions and decide who gets access to national security secrets. 
 
 In addition to Mr. Snowden, the company performed the background check for Aaron Alexis, a 34-year-old military contractor who killed 12 people at the Washington Navy Yard last year. Mr. Alexis, who died in a shootout with the police, left behind documents saying the government had been tormenting him with low-frequency radio waves. 
 
 The accusations highlight not just how reliant the government is on contractors to perform national security functions, but also how screening those contractors requires even more contractors. U.S. Investigations Service, now known as USIS, is the largest outside investigator for government security clearances. It is one of many companies that has found lucrative government work during the expansion of national security in the last decade. 
 
 From 2008 to 2012, about 40 percent of the company’s investigations were fraudulently submitted, the Justice Department said. 
 
 The government made the accusations in a 25-page complaint filed in United States District Court in Montgomery, Ala., where USIS has been the subject of a whistle-blower lawsuit since 2011. News that the government officially joined that case on Wednesday was reported by The Wall Street Journal. 
 
 Government lawyers accused the company of releasing investigations that had not been complete, a practice referred to in court documents as “dumping.” The government quoted from internal company emails to argue that the practice was widespread. 
 
 “Have a bit of a backlog building, but fortunately, most people are off this week so no one will notice!” one USIS employee wrote in 2010. 
 
 A spokesman for USIS said Thursday morning in a statement: “These allegations relate to a small group of individuals over a specific time period and are inconsistent with the strong service record we have earned since our inception in 1996. Since first learning of these allegations nearly two years ago, we have acted decisively to reinforce our processes and management to ensure the quality of our work and adherence to OPM requirements. We appointed a new leadership team, enhanced oversight procedures, and improved control protocols. From the outset, we have fully cooperated with the government’s investigation and remain focused on delivering the highest quality service under our OPM contracts.” 
 
 In September, former and current USIS employees detailed how the company had an incentive to rush work because it is paid only after a file is marked “FF,” for fieldwork finished, and sent to the government. In the waning days of a month, investigations were closed to meet financial quotas, without a required review by the quality control department, two former senior managers said at the time. 
 
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 The federal Office of Personnel Management confirmed that it paid USIS on a piecework basis. “The vendor is paid upon the delivery of a completed case,” the agency said in a statement shortly after the navy yard shooting. People familiar with the contract said it was intended to give the company an incentive to be efficient. 
 
 The 2007 background report done by USIS on Mr. Alexis showed that investigators learned he had been arrested three years earlier in Seattle, but the report did not include the crucial information that he had shot the tires of a construction worker’s car in what he told the police was an anger-fueled blackout. Mr. Alexis was given a secret security clearance in 2008, which was still valid on Sept. 16 when he stalked and killed a dozen victims at the navy yard with a sawed-off shotgun before the police killed him. Investigators relied on an interview with Mr. Alexis, who claimed he had only deflated the construction worker’s tires, Merton W. Miller, an associate director for investigations in the personnel office, said in a statement. 
 
 USIS also conducted the most recent security investigation of Mr. Snowden, in 2011. Patrick E. McFarland, the inspector general of the personnel office, told a Senate hearing in June that “there may be some problems” with the Snowden investigation, but he declined to give details. ||||| Aaron Alexis, 34, has been identified by officials as the gunman in Monday’s shooting at the Washington Navy Yard. In 2010, Alexis was arrested by Fort Worth police after a bullet was fired through the floor of his upstairs neighbor’s apartment. He told police that his gun accidentally discharged while he was cleaning it, and no charges were pursued. 
 
 Aaron Alexis, 34, has been identified by officials as the gunman in Monday’s shooting at the Washington Navy Yard. In 2010, Alexis was arrested by Fort Worth police after a bullet was fired through the floor of his upstairs neighbor’s apartment. He told police that his gun accidentally discharged while he was cleaning it, and no charges were pursued. Fort Worth Police Department/via AFP/Getty Images 
 
 Authorities say the former Navy reservist, who had been living in Fort Worth, was the dead gunman at the Washington Navy Yard. 
 
 Authorities say the former Navy reservist, who had been living in Fort Worth, was the dead gunman at the Washington Navy Yard. 
 
 Authorities say the former Navy reservist, who had been living in Fort Worth, was the dead gunman at the Washington Navy Yard. 
 
 The military’s beleaguered background-check system failed to block Navy Yard gunman Aaron Alexis from an all-access pass to a half-dozen military installations, despite a history of arrests for shooting episodes and disorderly conduct. 
 
 Alexis, a military contractor working on a computer project, used his secret-level clearance to gain entry to the Washington Navy Yard on Monday, where officials said he gunned down a dozen people before being killed by police. 
 
 The revelations about Alexis’s troubled past — and his ability to pass the government’s security-check system — prompted multiple examinations Tuesday into how background checks are conducted and how long a security clearance can last without review. The system was already under scrutiny after leaks of classified documents by fugitive National Security Agency contractor Edward Snowden. 
 
 President Obama directed his budget office to conduct a government-wide review of security standards for contractors and employees across federal agencies. Defense Secretary Chuck Hagel also ordered a broad review into security and access to military installations worldwide. 
 
 More than 24 hours after the deadly rampage, there was still widespread confusion over how Alexis managed to escape scrutiny since being given access to classified materials and facilities five years ago. The private contractor that most recently employed him pointed the finger at the Defense Department, which defended its handling of the case. 
 
 Alexis was granted secret-level security clearance in March 2008, when he was working as a full-time Navy reservist, according to the Pentagon. He was discharged from the Navy in January 2011 after a series of run-ins with his military superiors and police. 
 
 In September 2012, a Hewlett-Packard subcontractor called The Experts hired Alexis and said it confirmed his security clearance with the Defense Department. Thomas Hoshko, the company’s chief executive, said he confirmed the status again in late June of this year, when Alexis returned to work for the firm after a brief hiatus. 
 
 A background check done by a private contractor at the time turned up only a minor traffic violation, according to Hoshko. “It came back clean,” he said. 
 
 Alexis worked as a subcontractor helping to update and replace computers for Navy and Marine Corps installations. Since July, the 34-year-old had worked at six different naval locations, including facilities in Arlington, Va., Cherry Point, N.C., and Stafford, Va. He worked at the Navy Yard for several days before the shooting. 
 
 It is unclear why the Defense Department approved Alexis’s security clearance after his 2004 arrest in Seattle for shooting out the tires of a car. Thomas Richards, a spokesman for the Office of Personnel Management, said the office conducted only one security review of Alexis, in 2007, and that it turned up his 2004 arrest in Seattle. 
 
 He maintained his clearance despite more recent brushes with the law and a pattern of misconduct that preceded his discharge from the Navy. Alexis was arrested on charges of disorderly conduct in DeKalb County, Ga., in 2008, and after he fired a shot into his apartment ceiling in Texas in 2010. 
 
 A Defense Department official said that lower-level clearances such as the one granted to Alexis are typically good for 10 years. Former military employees who become private-sector contractors can also maintain their clearance during that time. 
 
 The official said a person can keep a clearance “in the absence of unadjudicated derogatory information.” 
 
 The agency did not conduct a new background check either last year, when Alexis was first hired as a military contractor, or this summer, when Alexis was seeking a second stint with the contracting firm, people familiar with his hiring said. Instead, the company hired an approved background screening firm that confirmed with the Defense Department that Alexis’s security clearance remained valid. 
 
 A secret-level clearance requires far less-intensive digging than one for top-secret clearance, and involves only a check of the FBI database, military records and data from law enforcement agencies where an applicant has lived, worked or attended school during the past five years. It does not require interviews with family members, co-workers or employers. 
 
 Hoshko told The Washington Post that he would not have hired Alexis if he had known about his arrests. 
 
 “Anything that suggests criminal problems or mental-health issues, that would be a flag,” he said. “We would not have hired him.” 
 
 No one in the company was made aware of the past incidents, he said. “If there’s not full disclosure on this, how do they expect us to make good decisions about who to trust and hire?” 
 
 Hoshko said his company and other contracting firms rely on the military to approve the security clearances of their employees, and he fears that budget crunches have led to faster and less thorough checks. His company hired a private firm — in September 2012, when Alexis first came to The Experts, and in June 2013, when he returned for another stint — to conduct a criminal background check of Alexis. As part of the company’s standard procedure for hiring new employees and rehiring old ones, the company also verified with the Defense Department both times that Alexis’s security clearance remained in force and conducted new drug tests. 
 
 Congressional leaders on Tuesday called for investigations and hearings into how the military screens contractors for classified work and entry to its bases. Sen. Kelly Ayotte (R-N.H.) asked the Senate Homeland Security and Governmental Affairs Committee to hold a hearing into contractor hiring practices at military installations, while Sen. Claire McCaskill (D-Mo.) wrote to Navy Secretary Ray Mabus seeking answers about oversight of contractor access and flaws in security clearances. 
 
 A report released Tuesday by the Defense Department’s inspector general also found serious deficiencies in a Navy screening program for people who didn’t have standard credentials. The program does not apply to contractors such as Alexis, but congressional staffers say it indicates another serious deficiency in the screening system. 
 
 Auditors found 52 convicted felons who received routine, 
 
 unescorted access to naval facilities through the program, known as the Navy Commercial Access Control System. The inspector general said the program, developed in 2010 to check the credentials of occasional contractors, created “a false sense of security” and should be abandoned immediately. 
 
 In one example, the report said an individual was given unescorted access to a base in 2011 for more than three months before it was discovered he had been convicted years earlier of “indecent liberties with a child,” a felony. Several other felonies also weren’t caught in the screening, including convictions for assault, theft and “throwing a missile at an occupied vehicle.” 
 
 Hoshko said he was disturbed to learn from The Post and other news outlets about police reports alleging that Alexis shot out a construction worker’s tires in Seattle in 2004 and fired a bullet into the ceiling of his Fort Worth apartment in 2010. 
 
 “If I can find this out just by doing a Google search, that is sad,” Hoshko said. “Anything that suggests criminal problems or mental-health issues, that would be a flag. We would not have hired him.” 
 
 Sen. Jon Tester (D-Mont.) received staff briefings on the case Tuesday and has authored legislation that would provide more funding to ferret out screening flaws. 
 
 “Corners are obviously being cut,” Tester said. “We had Snowden earlier this year and now the Navy Yard tragedy. We have to fix this.” 
 
 Sen. Thomas R. Carper (D-Del.) chairman of the Homeland Security and Governmental Affairs Committee, said he plans to investigate “a number of things” in the coming weeks — especially how Alexis could have been employed by a federal contractor despite his arrest records and treatment for mental illness. 
 
 “What is the responsibility of our government and contractors to vet employees and from time to time reinvestigate those employees, if concerns arise about someone?” Carper asked. “What kind of clearance or clearances did this suspect possess? What kind of background check did he undergo in order to get his clearance? Were his clearances up to date? Is there some quality problem with the quality process of granting those clearances? And maybe a third one is what can we learn from this incident to help make this installation and other military installations and federal buildings safer, so that some good could come out of something that was awful.” 
 
 Hoshko, whose company is based in Fort Lauderdale, Fla., said he applauds Congress’s revived interest in the rigor of security clearances, the vast majority of which are handled by private firms. 
 
 “You have to more seriously look at the people’s backgrounds,” Hosh­ko said. “If he had a mental background, we would have wanted to know it. . . . The whole [security clearance process] needs to be reviewed top to bottom.” 
 
 Alexis began working for The Experts as an hourly computer technician in September 2012 at a U.S. military base in Japan and finished his work in Japan in January 2013. 
 
 “There were no incidents,” Hosh­ko said. “The guys liked him.” 
 
 He took a break, according to co-workers, because he wanted to go back to school. 
 
 He returned to work on The Experts’ subcontract in July. Alexis told one of his colleagues that he was returning to the contracting world “because school didn’t pay,” Hoshko said. 
 
 Marjorie Censer, Alice Crites, Ed O’Keefe and Craig Whitlock contributed to this report.
– If giving a thumbs up to Edward Snowden and US Navy Yard shooter Aaron Alexis didn't get US Investigations Services kicked off the federal government's Christmas card list, it's definitely off now. The Justice Department yesterday accused the contractor, which handles roughly 45% of federal background checks, of fraudulently submitting more than 660,000 investigations, the Wall Street Journal and New York Times report. That's roughly 40% of all the work it did for the government over a four-year stretch—and doesn't even appear to include Snowden or Alexis. In a practice known as "flushing," the company would simply mark investigations as complete when they weren't, according to the feds. "Flushed everything like a dead goldfish," one USIS official is quoted as saying in the complaint. In another email, an employee wrote, "Have a bit of a backlog building, but fortunately, most people are off this week, so no one will notice!" The Justice Department is accusing former executives of encouraging these practices, which, according to whistleblowers, were designed to meet financial quotas. The company was paid per investigation it completed. The allegations first came to light in a 2011 whistleblower suit, which the government yesterday joined. The company says it has "acted decisively to reinforce our processes" in the years since.