Microwave diathermies (MWDs) are electromagnetic (EM) radiation emitting systems that are used by physiotherapists for thermotherapy treatment. Although this form of therapy is widely available in most physiotherapy units worldwide, management of the equipment is not obligatory addressed either by clinical engineers or medical physicists. A novel quality control (QC) protocol for MWD equipment, examining mechanical, electrical and electronic condition, the power output and EM radiation distribution in the electrotherapy room, was used during a national QC survey. The results of the survey revealed serious concerns about the safety of users and coexisting patients. The proposed approach could result in the introduction of EM-screened rooms, ensuring that MWD users and other persons in the vicinity will not be exposed to EM radiation over reference levels. International bodies could develop specific directives for EM radiation exposure in Physiotherapy Units, to conform to the proposed acceptance and functioning criteria for MDWs.