The suit filed Wednesday says that Sanofi used contracts that appeared to be for legitimate purposes to direct money to hospitals, doctors and retail pharmacy chains to induce them to purchase and prescribe Sanofi's diabetes medication. It also claims that "approximately $1 billion is missing from Defendant Sanofi which has not been accounted for."
Sanofi itself in October cited poor relations between Viehbacher and the board as the reason he was sacked.
Read MoreSanofi ousts CEO after warning on diabetes business
The bombshell new kickback allegations by a Sanofi paralegal named Diane Ponte—who herself was fired in September after allegedly suffering retaliation for bringing the scheme to light—come two years after the drug company reached an agreement with the Justice Department and several states to pay $109 million to settle claims that it engaged in kickbacks by giving doctors free samples of an arthritis drug as a way to encourage them to buy and prescribe that medication.
Such kickbacks are illegal because they can encourage the prescription of drugs that are covered by federal Medicare and Medicaid insurance programs, and thus have taxpayers foot the bills for medication that might otherwise not have been prescribed.
After that 2012 settlement, Sanofi also had a corporate integrity agreement with the Health and Human Services Department requiring the company to abide by federal health-care laws and to report illegal activities by the company and its employees, Ponte's suit said. However, a check of HHS' database of such integrity agreements indicated that pact had not been executed as of yet.
Sanofi on Wednesday indicated it had not yet been served with Ponte's lawsuit, but in a statement said, "Sanofi does not comment on litigation."
On Thursday, after reviewing the suit, Sanofi issued a new statement, which said: "Diane Ponte is a disgruntled former employee who is opportunistically attacking our company. Ponte filed for violations of New Jersey state employment law, specifically the New Jersey Conscientious Employee Protection Act ('CEPA')."
"The employment law allegations are without merit, and Sanofi will vigorously defend the suit. We take this matter very seriously and will protect our company and our reputation," Sanofi said.
Ponte's suit, filed in New Jersey Superior Court in Newark, names as defendants Sanofi, Viehbacher, Sanofi General Counsel Robert DeBerardine and other executives, including Sanofi's former vice president of its U.S. diabetes business, Dennis Urbaniak, and the ex-assistant vice president of special projects, Raymond Godleski.
"It's shocking that these people got away with this for so long and then fired this woman for uncovering their wrongdoing," said Rosemarie Arnold, lawyer for the 53-year-old Ponte. "She was blatantly fired as a result of her whistleblowing activity."