The company that handled a background check on National Security Agency leaker Edward Snowden allegedly defrauded the US government by submitting at least 665,000 investigations that had not been properly completed.

That figure, the justice department said Wednesday in a civil complaint, amounts to 40% of the cases that the company, US Investigations Services Inc (USIS), sent to the government over a four-year span, continuing through at least September 2012.

In response, the company said that integrity and excellence are core values at USIS, which has 6,000 employees.

The government said that 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 $11.7m in performance awards for the years 2008, 2009 and 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's 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 chief executive.

The background investigations that were dumped spanned most government agencies — including the justice department, the department of homeland security, the defense department, the defense intelligence agency, the department of health and human services, the transportation department and the treasury department.

The dumped background investigations involved checks of applicants' credit histories, legal records and checks of government agency files such as FBI files and fingerprint records. The dumped investigations also included interviews of employers and co-workers and others associated with the subject of the investigation.

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

Initially, the justice department said, USIS would dump cases manually. Later, it began using a software program called Blue Zone which enabled USIS to identify a large number of background investigations, quickly make an electronic "review complete" notation and then give the cases to the government. Dumping, the justice department said, occurred daily.

USIS conducts hundreds of thousands of background checks for government employees and has more than 100 contracts with federal agencies. One employee it screened was Aaron Alexis, the gunman accused of killing 12 people and himself at the Washington Navy Yard last September. Alexis had been given a security clearance in 2008.