Under the consent decree filed in US District Court in Connecticut, Pfizer certifies the violations have been corrected. But the violations undermined EPA's ability to determine compliance, the agency said in a statement.

The alleged violations, which occurred between October 2002 and December 2005, resulted from a failure of Pfizer's leak detection and repair program, which presented the risk of excess emissions of hazardous air pollutants, the Justice Dept. and EPA said in a news release.

During its production of pharmaceutical-grade chemicals, Pfizer used substances such as methanol, hydrogen chloride, methylene chloride, MTBE, hexane, toluene and many others, which are classified by EPA as hazardous air pollutants.

"All facilities that produce hazardous air pollutants must carefully adhere to all provisions of EPA's Clean Air requirements to ensure that we are taking every necessary step to protect human health and our environment," Robert Varney, regional administrator of EPA's New England office, said in a statement.

Pfizer, the world's largest drug maker, said in a statement it agreed to pay the civil penalty, even though it "believes that the penalty sought by the government is not commensurate with the nature of the alleged violations."

Pfizer said it took timely steps to enhance compliance of its program and ensure the agency's concerns were addressed. In addition, the drug maker said it has no reason to believe "that the alleged deficiencies resulted in any environmental harm."

The specific violations included a failure to properly conduct pressure tests to identify leaks, repair leaks before start-up, equip open-ended lines with a cap or other seal and document leak tests to establish full compliance with requirements, the news release said.

The Groton facility that was cited ceased pharmaceutical manufacturing in January. (Reporting by Bill Berkrot; Editing by Andre Grenon)