A modular safety shelter provides protection from fragment, overpressure, radiation, and toxic hazards through a combination of physical design of modular segments, of joint seals between modular segments, of door assemblies, and of HVAC control systems. The modular shelter is formed of two or more prefabricated concrete modular segments each including a built-in foundation, roof, and side walls, and a prefabricated concrete vestibule segment providing an airlock-like access to the shelter. The prefabricated modular segments and vestibule segment are transported to a site and assembled to each other on-site to provide a fully enclosed space within the modular shelter. A multi-layer joint seal is formed between adjacent modular segments to prevent ingress of toxic, flammable, or thermal hazards. An integrated HVAC controller monitors toxic or flammable hazards outside and inside of the shelter, and controls HVAC systems to minimize spread of contaminants upon detecting a hazard.