“We made mistakes,” Jeff Eller, a spokesman for the company, said in a statement. “And RDC understands that these mistakes, directed by former management, have serious consequences.”

The two former company officials, Laurence F. Doud III and William Pietruszewski, were also charged with conspiring to distribute drugs and defrauding the government.

Mr. Pietruszewski, 53, of Oak Ridge, N.J., who was the chief compliance officer, was also charged with failing to file reports to the authorities about suspicious orders for controlled substances. He pleaded guilty last week and is cooperating with prosecutors.

Mr. Doud, 75, the former chief executive officer, pleaded not guilty late Tuesday in United States District Court in Manhattan and was released on a $500,000 bond. If convicted, Mr. Doud faces a mandatory 10-year minimum sentence and a maximum of life in prison.

The charging documents portray a company largely animated by Mr. Doud’s greed. As chief executive, he drove up the sales of oxycodone pills up ninefold over four years, from 4.7 million in 2012 to 42.2 million in 2016.

Fentanyl sales shot up even more over the same period, to 1.3 million doses from 63,000 doses, the documents said. And Mr. Doud’s compensation, tied to the sales, more than doubled, climbing to over $1.5 million.

Mr. Doud’s lawyer, Robert C. Gottlieb, said other executives at the company were scapegoating his client for their misdeeds. “Mr. Doud is being framed by others to cover up their wrongdoing,” Mr. Gottlieb said in a statement. “The government has it all wrong. He will fight these charges to his last breath and he will be vindicated.”