(CNN) -- U.S. prosecutors have filed charges against a security company, accusing it of faking completed background checks to bilk the government of millions of dollars.
U.S. Investigations Services used a computer program to "flush" or "dump" background checks -- labeling them as completed, when in fact they had not carried out a quality review as required by the government contract, prosecutors allege in a complaint.
The fraudulent behavior involved at least 665,000 background investigations -- about 40% of the total number the company conducted, prosecutors allege.
The company received nearly $12 million in bonus payments from 2008 through 2010, which would not have been given if the U.S. Office of Personnel Management had known of USIS's actions, the complaint says.
USIS is charged with three counts: false or fraudulent claims; false statements, and breach of contract.
Other filings -- including by the defense -- remain sealed.
A USIS spokeswoman described the "alleged conduct referenced in the civil complaint" as "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."
After the company learned of the allegations nearly two years ago, it "acted decisively to reinforce our processes and management to ensure the quality of our work and adherence to OPM requirements."
"We appointed a new leadership team, enhanced oversight procedures, and improved control protocols. From the outset, we have fully cooperated with the government's investigation and remain focused on delivering the highest quality service under our OPM contracts," the spokeswoman said.
On its website, USIS describes itself as "the leading industry provider of background investigations to the federal government, with a long-standing reputation for service, quality and timeliness." The spokeswoman said "integrity and excellence are core values at USIS that guide the work of our outstanding 6,000 employees."
CNN's Josh Levs and Jonathan Helman contributed to this report.