The chemist, whose name wasn't reported, handled some 2,600 cases for 80 law enforcement agencies in 35 Florida counties and 12 judicial circuits for the Florida Department of Law Enforcement's Pensacola Regional Crime Laboratory since 2006, CNN reported.
Last week, investigators discovered prescription pain pills were missing from the evidence room at the Escambia County Sheriff's Office. Prescription pills had been replaced with over-the-counter medication in more than one of the chemist's cases.
The finding could compromise drug convictions, Florida Attorney General Pam Bondi said.
"Our battle against prescription drug abuse in Florida has been very successful over the last three years, and I will not tolerate any actions that compromise our continued success in ridding our state of this problem," she said. "This situation simply underlines the extent of the problem our country faces with prescription drug abuse."