The Justice Department filed a lawsuit on Thursday against AmerisourceBergen, one of the country’s largest pharmaceutical manufacturers, accusing the company of knowingly distributing opioids that were later resold illegally.

The suit, filed by the department’s civil division in conjunction with federal prosecutors in New Jersey, Colorado, Pennsylvania and New York, is part of a growing effort by federal agencies to hold drug companies accountable for their role in the nation’s opioid crisis. It accuses AmerisourceBergen and two of its subsidiaries of “at least hundreds of thousands” of violations of the Controlled Substances Act. If the company is found liable, it could face billions of dollars in fines, according to Vanita Gupta, the associate attorney general overseeing the civil division.

Under federal law, wholesale drug distributors like AmerisourceBergen are obligated to report “suspicious” orders of controlled substances to the Drug Enforcement Administration. An order is considered suspicious if it is an unusual size or does not follow the normal pattern or frequency, or if it raises other concerns, such as the legitimacy of a customer’s business.

In an 80-page complaint, filed in Federal District Court for the Eastern District of Pennsylvania, the Justice Department accused AmerisourceBergen of failing to report many of these suspicious orders for nearly a decade, in what it described as an “egregious failure” that had contributed to the opioid epidemic.

More than 90,000 people died in the United States from drug overdoses in 2020, according to the Centers for Disease Control and Prevention. Opioids were involved in close to 75 percent of those deaths.

In the complaint, investigators cited five examples of violations, including at two pharmacies, one in Florida and one in West Virginia, where they said AmerisourceBergen knew that its drugs were likely being sold in parking lots for cash. They also cited violations involving pharmacies in New Jersey whose employees had been charged with drug offenses.

A fifth pharmacy, in Colorado, was the largest purchaser of oxycodone 30-milligram tablets in the state; investigators said that AmerisourceBergen knew this and continued to supply the pharmacy, even though 11 of its customers were identified as possibly having drug addictions. At least two of them later died of overdoses, according to the complaint.

The lawsuit is separate from a federal criminal inquiry into the company’s actions and a $26 billion settlement reached in February by several drug companies, including AmerisourceBergen, based in Conshohocken, Pa., in thousands of civil claims in state courts related to the opioid crisis.

“For years, AmerisourceBergen put its profits from opioid sales over the safety of Americans,” said Philip R. Sellinger, the U.S. attorney for the district of New Jersey, in a call with reporters.

“This was part of a brazen, blatant and systemic failure by one of the largest companies in America to comply with its obligations to report suspicious opioid orders, contributing to the epidemic of opioid abuse throughout this country,” he added.

Jacqueline C. Romero, the U.S. attorney for the Eastern District of Pennsylvania, said the allegations against the company were especially disturbing, given that its headquarters were only a few miles from neighborhoods in Philadelphia devastated by the opioid epidemic.

In a statement Thursday, AmerisourceBergen said the complaint “focuses on five pharmacies that were cherry-picked out of the tens of thousands of pharmacies that use AmerisourceBergen as their wholesale distributor, while ignoring the absence of action from former administrators at the Drug Enforcement Administration — the D.O.J.’s own agency.”

The company said that it had verified the registration and licenses of the five pharmacies before filing any orders; conducted “extensive due diligence” into the customers; and reported the sales and hundreds of suspicious orders of controlled substances to the D.E.A.

“With the vast quantity of information that AmerisourceBergen shared directly with the D.E.A. with regards to these five pharmacies, the D.E.A. still did not feel the need to take swift action itself,” the company said, adding that it had terminated relationships with four of the pharmacies before the agency took action against them.

AmerisourceBergen reported revenue of $214 billion in 2021.

Prosecutors said that company executives reported only a fraction of suspicious transactions, despite knowing that many of their pills were being diverted to the illegal market, according to the complaint.

The complaint said that AmerisourceBergen executives ignored red flags of drug diversion and relied on inadequate internal systems to monitor suspicious orders. It also accused the company of intentionally altering records to reduce the number of controlled substances reported as suspicious.

If AmerisourceBergen is found liable, it could face up to $10,000 for each reporting violation before November 2015; up to $16,864 for each violation between November 2015 and October 2018; and up to $109,374 for each violation after October 2018, the Justice Department said.