Steven Brandenburg, 46, of Grafton, Wisconsin, faces up to 20 years in person on two counts of attempting to tamper with consumer products with reckless disregard for the risk that another person will be placed in danger of death or bodily injury, the Justice Department said in a statement.
Brandenburg's attorney declined to comment about the deal.
"The FDA has ensured that the Moderna COVID-19 vaccine meets the agency's rigorous standards for quality, safety, and efficacy," FDA Assistant Commissioner for Criminal Investigations Catherine A. Hermsen said in a statement.
About 57 doses from the tampered vials were distributed to patients, according to federal prosecutors.
Brandenburg was arrested on New Year's Eve. He was released conditionally to his home four days later after Wisconsin prosecutors said they needed more time for test results from Moderna to determine the exact damage the pharmacist caused when he tampered with the 57 vials, each of which contained about 100 doses.
Last week, Ozaukee County District Attorney Adam Gerol said tests were still ongoing, but "the best evidence at this point is that the vaccine remains viable."
Brandenburg's sentencing hearing has not yet been scheduled.