In Florida, regulatory authority over medical waste is shared between The Department of Environmental Protection and the Department of Health. The Department of Environmental Protection has primary responsibility for biomedical waste incineration and final disposal. The Department of Health has primary authority and responsibility for facilities that generate, transport, store, or treat biomedical waste through processes other than incineration. Section 381.0098, Florida Statutes and Chapter 64E-16, of the Florida Administrative Code (FAC) provides guidance to facilities that generate biomedical waste to aid them in ensuring proper management of that waste. Aspects of medical waste management are also controlled by the Occupational Safety & Health Administration (federal and/or state) and Department of Transportation (federal and state).

Biomedical waste generators are required to maintain a Biomedical Waste Operating Plan, encompassing an emergency contingency plan, spill decontamination procedures, and a Spill Cleanup Standard Operating Procedure (SOP). Exterior waste storage must be securely locked and exhibit biohazard warning symbols. Waste removal should occur within 30 days of the initial placement of a non-sharps item into a red bag/sharps container or upon sealing a sharps-only container, commencing from the day of waste collection. Interior storage spaces must be waterproof, have controlled access, and be devoid of carpeting; rough cement surfaces must be sealed. Containers should be disposed of within 30 days of closure. Biomedical waste training must be administered initially and annually, with training details and records integrated into the Biomedical Waste Plan. An annual generator permit is mandatory, visibly displayed within the facility. Exemptions are applicable for generators generating less than 25 lbs. of waste in a 30-day period for up to 12 months. Even facilities exempted from this regulation must first procure a permit, maintain records for one year, substantiate their exempt status, and submit an Exemption Application using DOH form 4089.