BACKGROUND Effective management of modern public health emergencies requires the coordinated efforts of multiple agencies representing various disciplines. Organizational culture differences between public health (PH) and emergency management (EM) entities may hinder inter-agency collaboration. We examine how PH and EM differ in their approach to PH law and how such differences affect their collaboration towards PH preparedness. METHODS We conducted 144 semi-structured interviews with local and state PH and EM officials between April 2008 and November 2009. Thematic qualitative analysis in ATLAS.ti was used to extract characteristics of each agency's approach to PH legal preparedness. RESULTS Two conflicting approaches to the law emerge. The PH approach is characterized by perceived uncertainty regarding legal authority over preparedness planning tasks; expectation for guidance on interpretation of existing laws; and concern about individual and organizational liability. The EM approach reveals perception of broad legal authority; flexible interpretation of existing laws; and ethical concerns over infringement of individual freedoms and privacy. CONCLUSIONS Distinct interpretations of preparedness law impede effective collaboration for PH preparedness. Clarification of legal authority mandates, designation within laws of scope of preparedness activities and guidance on interpretation of current federal and state laws are needed.