The company that handled a background check on National Security Agency leaker Edward Snowden allegedly defrauded the government by submitting at least 665,000 investigations that had not been properly completed, and then tried to cover it up when the government suspected what was going on.

The number of investigations, the Justice Department said Wednesday in a civil complaint, amounts to 40 percent of the cases that the company, U.S. Investigations Services Inc., sent to the government over a four-year span, continuing through at least September 2012.

USIS was involved in a background investigation of Snowden in 2011, but his particular job doesn’t figure in the lawsuit.

In a statement, USIS said “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.”

The statement said the company first learned of the allegations nearly two years ago and that USIS has appointed a new leadership team, enhanced oversight procedures and has fully cooperated with the government’s investigation. The company said that “integrity and excellence are core values” at USIS, which has 6,000 employees.

The government said USIS engaged in a practice known inside the company as “dumping” or “flushing.” It involved releasing uncompleted background cases to the government and representing them as complete in order to increase revenue and profit.

The government paid the company $11.7 million in performance awards from 2008 to 2010, according to the Justice Department court filing.

USIS senior management “was fully aware of and, in fact, directed the dumping practices,” the government complaint said. Beginning in March 2008, USIS’ president and CEO established revenue goals for the company. USIS’s chief financial officer determined how many cases needed to be reviewed or dumped to meet those goals, the complaint added.

The number of cases that needed to be reviewed or dumped to meet revenue goals was conveyed to the firm’s vice president of field operations and to the president of investigative service division, the complaint said.

According to one internal company document, a USIS employee said, “They will dump cases when word comes from above, such as from” the president of the investigative service division and the president and CEO.

According to the complaint, USIS would dump reports of investigations knowing that there could potentially be quality issues associated with those reports.

“If the allegations are true, allowing somebody who is not qualified to access classified information is just simply awful, and is potentially dangerous,” said Alexander Brittin, a government contracts attorney for the past 30 years. “If this company is not doing background checks correctly, who knows what’s getting through?”