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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. ||||| WASHINGTON—The Justice Department on Wednesday accused the government's largest private security background check contractor of defrauding the country of millions of dollars by methodically filing more than 660,000 flawed background investigations—40% of the cases it sent to the government over a four-year period. 
 
 Prosecutors accused former top US Investigations Services LLC executives of directing improper practices that became a...
– 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.