WASHINGTON — U.S. Investigations Services (USIS) allegedly defrauded the federal 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 company, headquartered in Falls Church, Va., has an office in Boyers and two offices in Grove City.

Those two offices employ a total of 1,500 of the company’s 6,000 workers.

The number of improper investigations amounts to 40 percent of the cases that USIS sent to the government over four years, continuing through at least September 2012, the Justice Department said Wednesday in a civil complaint.

USIS was involved in a background investigation of National Security Agency leaker Edward Snowden in 2011, but his 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 cooperated with the government’s investigation. The company said that “integrity and excellence are core values” at USIS.

The government said that USIS engaged in a practice known in the company as “dumping” or “flushing.” It involved releasing uncompleted background cases to the government and representing them as complete 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’ 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 with those reports.

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

The company is a contractor for the federal Office of Personnel Management (OPM), which is responsible for background investigations of current or prospective federal employees and contractors.

USIS concealed its dumping practices from OPM, according to the government’s court papers.

In April 2011, OPM raised concerns with USIS after tests showed that a large number of investigation reports were identified as complete when computer metadata revealed that the reports had never been opened by a reviewer. In a response to OPM, USIS falsely attributed the problems to a variety of software issues, said the Justice Department filing.

In addition, USIS ensured that all dumping practices stopped when OPM was on site conducting audits, but then resumed after OPM’s auditors were gone, the government alleged.

USIS does hundreds of thousands of background checks for government employees and has more than 100 contracts with federal agencies.