In 2006, flea-borne rickettsiosis (flea-borne typhus), a zoonotic disease caused by either Rickettsia typhi or R. felis and transmitted primarily by two flea species, the Oriental rat flea and the cat flea, re-emerged as an important vector-borne disease in Orange County, California. The Orange County Mosquito and Vector Control District (OC Vector Control) has investigated 142 human cases of flea-borne rickettsiosis. Results of these investigations have established a link with Rickettsia-infected cat fleas, opossums, feral cats, and disease transmission to humans; no cases have been associated with rats and their fleas. Since initiation of a Trap-Neuter-Return (TNR) Program by Orange County (OC) Animal Care in 2009, OC Vector Control has been working with OC Animal Care to minimize the potential public health risks associated with the TNR Program. Interagency discussions have led OC Animal Care to prohibit the release of TNR cats at locations with a high risk for zoonotic disease transmission to humans, such as schools, parks, and health care facilities, and also to disclose the release sites to OC Vector Control. OC Animal Care has not agreed to OC Vector Control’s request for a zoonotic disease review of its TNR Program, nor has it provided a procedural manual to verify the verbal agreements reached by the two agencies. In agreement with OC Vector Control’s concerns, an investigation in 2015 by the Orange County Grand Jury of OC Animal Care’s TNR Program recognized the Program’s potential to increase zoonotic disease transmission to the public and other wildlife. We discuss the conflicting views arising from two governmental agencies, which perceive the zoonotic diseases risk associated with a TNR program at significantly different thresholds of concern.