Infections acquired in research laboratories and unintentional pathogen escapes from breaches in biocontainment pose risks to humans and the environment, necessitating the need for effective biosafety and biosecurity management frameworks in biocontainment research animal facilities (BRAFs). We examine key biosafety issues associated with BRAFs, including inadequate decontamination procedures for wastewater and experimental samples, handling high biosafety level pathogens in lower-level laboratories, risks of animal bites and sharps injuries, contamination of bedding and enrichment materials, and improper management and transportation of biohazard samples. Additionally, we discuss the role of veterinarians in research animal facilities and the challenges they encounter in maintaining biocontainment standards. We emphasise the importance of routine monitoring of effluent water to detect possible disease outbreaks. We recommend a thorough investigation of disease outbreaks to identify potential sources of pathogen release from BRAFs, which could serve as hotspots for future disease outbreaks. Findings from such investigations will inform the development of policies aimed at safeguarding human populations from future pandemics and preventing BRAFs from becoming sources of infectious disease outbreaks.