A Boston federal judge has imposed a $321.6 million criminal fine against Merck & Co. Inc. for its Vioxx promotion and marketing activities, bringing the company’s payout in recent months to nearly $1 billion for illegal marketing.

On April 19, Judge Patti Saris of the District of Massachusetts imposed the fine against Merck’s U.S. unit following its December 2011 guilty plea. Merck violated the Food, Drug and Cosmetic Act by introducing a misbranded drug into interstate commerce.

The sentencing ends the government’s multiyear investigation of Merck’s conduct concerning Vioxx, a pain reliever that was pulled from the market in September 2004 because of safety concerns.

Merck promoted Vioxx for rheumatoid arthritis for a nearly three-year period before the U.S. Food and Drug Administration approved it for that use in April 2002.

The April 19 sentence followed a November 2011 global resolution, which required Merck to pay $628.4 million to resolve other charges of off-label marketing of Vioxx and false statements about the drug’s cardiovascular safety.

That settlement included $426.4 million for the United States and nearly $202 million for participating states, which relied on the company’s false statements. The settlement included 44 states and the District of Columbia, according to a February U.S. Securities and Exchange Commission filing. According to Merck, Alaska, Kentucky, Montana, Pennsylvania, South Carolina and Utah did not participate in the settlement.

As part of the civil settlement, Merck also signed a corporate integrity agreement with the Office of Inspector General of the Department of Health and Human Services.

In a written statement, Carmen Ortiz, the U.S. attorney for the District of Massachusetts, said, “The severity of these criminal and civil sanctions should serve as a reminder of this office, and this department’s unwavering commitment to holding drug companies fully accountable for failures to comply with their public safety and marketing obligations, and to recovering taxpayer funds that have gone towards the purchase of illegally marketed products.”

Merck’s lawyers — Theodore Wells Jr., co-chairman of the litigation department at New York’s Paul, Weiss, Rifkind, Wharton & Garrison, and Jack Cinquegrana, who co-chairs the litigation department at Boston’s Choate Hall & Stewart — declined to comment.

“The government acknowledged Merck’s full cooperation throughout this lengthy seven-year investigation,” said Merck spokesperson Ron Rogers. “The second thing we want to say is that by resolving this matter, we’re better able to focus on what Merck does best, which is discovering and developing new medicines and vaccines that improve people’s lives around the world.”

Vioxx personal injury suits were even more expensive for Merck to resolve. In late 2007, the company agreed to pay $4.85 billion to resolve consumer class actions.

The company’s Vioxx saga continues with an Eastern District of Kentucky case it has brought against Kentucky Attorney General Jack Conway for using contingency fee lawyers to pursue the state’s Vioxx marketing case against the company. Merck accuses Conway of violating the company’s due process rights by hiring these lawyers to bring what it calls a “quasi-criminal enforcement proceeding” against it. In March, District Judge Danny Reeves denied Conway’s motion to dismiss the case.  

Sheri Qualters can be contacted at squalters@alm.com.