The Justice Department has filed a detailed complaint in a whistleblowers’ lawsuit it joined against the company that conducts security-background checks for nearly half of potential U.S. government hires, adding new detail to accusations that the firm knowingly conducted flawed investigations of indiduals seeking security clearances.

The filing against Falls Church-based USIS includes information about alleged shortcuts the company took in reviewing security-clearance candidates and about a cavalier and joking approach taken by some USIS employees to submitting files to the government that had not undergone a full review.

“Flushed everything like a dead goldfish,” one manager wrote in one of several e-mail messsages cited in the court filing.

The filing accuses USIS of submitting incomplete background reviews in about 40 percent of the cases it handled — at least 665,000 cases — and in the process qualifying for nearly $12 million in performance bonuses.

“Beginning in at least March 2008 and continuing through at least September 2012, 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 Justice Department said in the complaint, which was filed Wednesday in U.S. District Court in Alabama .

The cases were incomplete because they had not undergone a promised “quality review,” the government said.

USIS, in a statement, said the allegations did not fit the company’s record or approach.

“The alleged conduct referenced in the civil complaint is contrary to our values and commitment to exceptional service,” the company 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.”

In response to the allegations, which surfaced last year, “we appointed a new leadership team, enhanced oversight procedures, and improved control protocols,” the USIS statement continued. “From the outset, we have fully cooperated with the government’s investigation and remain focused on delivering the highest quality service.”

USIS conducted background checks for former National Security Agency contractor Edward Snowden and government contractor Aaron Alexis, who shot and killed 12 people at the Washington Navy Yard last fall.

However, congressional and executive branch inquiries have not found evidence that USIS cut corners when it vetted Alexis or Snowden, whose decision to leak thousands of classified government documents last year revealed the extent of surveillance by U.S. intelligence agencies. In the case of Alexis, an OPM official said last year that there were no red flags in the way his background investigation was conducted.

“OPM has reviewed the 2007 background investigation file for Aaron Alexis, and the agency believes that the file was complete and in compliance with all investigative standards,” said Merton W. Miller, OPM associate director for federal investigative services.

Still, USIS has drawn continued interest from lawmakers and the Justice Department. Separately, the company is under criminal investigation over “broad issues,” including whether it misled officials about the thoroughness of its work, according to federal officials.

A number of former USIS employees have been charged with falsifying records in individual cases. A USIS spokesperson declined to comment on the criminal inquiry Thursday; previously, the company denied knowledge of the criminal probe.

The federal government gave USIS nearly $2.4 million in bonuses in fiscal year 2008, $3.5 million in 2009 and $5.8 million in 2010 as a reward for good performance, the complaint says.

The complaint includes e-mails from company officials showing that they were motivated to show progress in approving personnel in order to receive bonus payments.

If the Office of Personnel Management had known about the shortcuts, it would not have deemed “USIS’s performance acceptable,” the complaint says.

The lawsuit that the government is joining was filed by Blake Percival, a former director of fieldwork services at USIS. He sued the company in 2011 under the whistleblower provisions of the False Claims Act, accusing the company of rushing cases through the system and hiding the practice from OPM.

The Justice Department first accused USIS of wrongdoing in October, when it “intervened” in the suit. Wednesday’s filing was first reported by The Wall Street Journal.

After the additional information in that case was filed this week, Sen. Claire McCaskill, D-Mo., issued a statement critical of the “stunning failures this company — and the resulting threats to our national security.”

McCaskill, a member of the Homeland Security and Government Affairs Committee, has introduced legislation with Sen. Jon Tester (D-Mont.) that would improve oversight of the security clearance process, proving more funds for auditing and investigation of contractors !