The alleged violations occurred at a former Pfizer manufacturing plant in Groton, Connecticut between October 2002 and December 2005.
PharmaMACT was implemented in an attempt to control emissions of hazardous air pollutants from pharmaceutical manufacturing operations.
Ronald Tenpas, assistant attorney general for the Justice Department's Environment and Natural Resources Division, said: "This significant penalty, the first in federal court under the PharmaMACT regulations, should send a strong message to the pharmaceutical industry that they must be diligent in detecting and repairing leaks of hazardous substances.
"We will not wait to enforce the law until after a catastrophe occurs. Penalties such as this one compel the industry's close attention and rigorous implementation of the leak detection requirements to prevent the escape of harmful air pollutants that can endanger the public."
The US Department of Justice listed violations associated with the production of bulk pharmaceutical materials. These included a failure to properly conduct pressure tests to identify leaks and repair them before start-up.
In addition there were failures to seal open-ended lines and document leak tests to comply with leak detection and repair (LDAR) requirements.
Pfizer has responded to the fine by saying it believes it to be excessive given the nature of the allegations. It also states its belief that the majority of the alleged violations were self-reported and steps were taken to address the concerns.
In addition the pharmaceutical behemoth highlights the point that the government has not asserted that the alleged violations resulted in environmental damage.
PharmaMACT was implemented under the federal Clean Air Act and was designed to impose "Maximum Achievable Control Technology" (MACT) standards upon the pharmaceutical industry.
These standards are designed to control the levels of hazardous air pollutants in order to avoid damage to human health or the environment. The pharmaceutical industry, as with other areas of business, is under increasing pressure to clean up its act.
Some within the industry have been responding to these pressures, with Pfizer itself supporting environmental technology projects through its Green Chemistry initiative.