The Department of Justice has accused the United States Investigations Services (USIS) of swindling millions of dollars from the government.

The USIS had also vetted whistleblower Edward Snowden previously and Aaron Alexis, the technology contractor who killed 12 people at the Washington Navy Yard in September 2013.

The courts filings reported that background checks conducted by the USIS were below agreed standards, according to Reuters.

The Department of Justice said in a filing, Wednesday, that between March 2008 and September 2012, the USIS filed at least 665,000 flawed background checks, almost 40 percent of the total submissions. Furthermore, it accused the USIS of using influence in the federal government to cover up its practice of "flushing background checks."

The whistleblower lawsuit filed in July 2011 by an ex-USIS employee under the False Claims Act was not about the firm's review of Snowden, according to Reuters. The lawsuit alleged that the USIS failed to perform adequate control reviews in connection with its background investigations.

"USIS management devised and executed a scheme to deliberately circumvent contractually required quality reviews of completed background investigations in order to increase the company's revenues and profits," the department said in its filing.

The firm used a special software, Blue Zone, to do a greater number of background checks in a shorter period of time. The USIS was paid on the basis of the number of investigations done by it in the range of $95 to $2,500. The Justice Department will try to recover the damages through the lawsuit, it said.