Permitting is split between the City of Rochester, which manages its own building and zoning services, and the county, which handles unincorporated areas and smaller municipalities. The county planning department oversees land use and zoning for rural areas, while specific environmental overlays such as shoreland and floodplain management are enforced across all jurisdictions.
How this fits with the state
The state authority here is Minnesota Department of Labor and Industry. The county file does not replace that — it adds the permit office, local overlays, and the actual filing path.