The Justice Department is accusing the contractor that conducted a background check for National Security Agency (NSA) leaker Edward Snowden of failing to properly review more than 660,000 cases.

Federal prosecutors said in a filing Wednesday that United States Investigations Services (USIS) fraudulently collected millions from the government for completing background checks that the company did not sufficiently review.

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The 25-page complaint joining a whistle-blower case against the USIS says the company “dumped” at least 665,000 background checks between March 2008 to September 2012, telling the government they were complete when they were not.

Those cases represented 40 percent of total background checks completed by the service, the complaint alleges.

The USIS received nearly $12 million in performance awards between 2008 and 2010 for completing background checks that were not properly reviewed, the Justice Department said.

Based in Falls Church, Va., the service conducted background checks on both Snowden and Aaron Alexis, the Washington Navy Yard shooter.

In a statement, it said the alleged conduct in the complaint was “contrary to our values and commitment to exceptional service.”

“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,” a USIS spokeswoman said. “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.”

The Justice Department complaint filed in U.S. District Court in Alabama, which was first reported by The Wall Street Journal Wednesday, joins a 2011 whistle-blower lawsuit from former USIS employee Blake Percival.

Last year the department said it would sign onto the lawsuit as the USIS came under greater congressional scrutiny in the wake of Snowden’s leaks of highly classified National Security Agency documents.

The complaint alleges that senior management knew of the dumping scheme, where cases were ranked on priority and the lowest-risk cases were “flushed” to meet its goals.

The complaint cited internal emails from employees conducting the fraudulent reviews.

“Shelves are as clean as they could get. Flushed everything like a dead goldfish,” one employee wrote in 2010.

“T’is Flushy McFlushershon at his merry hijinks again!!” another wrote.

Federal prosecutors say that USIS employees began using a program called “Blue Zone” to systematically mark the reviews as complete and send them to the Office of Personnel and Management, even if they had not gone through the review process.