The Philippines is identified as a natural disaster hot-spot and is ranked third among the most disaster risk countries in the world. Typhoons and tropical storms, flood, and earthquakes continue to cause thousands of human deaths and injuries in the country despite efforts of various organizations to intensify strategies for disaster risk reduction. Next to impacts on people, destructions in the critical infrastructure are often the most-compelling concerns in the aftermath of a disaster. This paper looked into the natural disaster preparedness of government and non-government organizations directly responsible for critical infrastructures operation and emergency management functions in Ozamiz City. The area was selected since commercial activities are centered on coastal areas and many of its population are located near the coastal area making it prone to the impacts of hydrological events. This study employed the survey method. Survey questionnaires were administered to 254 administrators and employees from 45 organizations and follow up interviews were conducted. Overall findings revealed that the organizations are moderately prepared for natural disasters. However, findings from the individual category of infrastructure showed that facilities, utilities and transportation organizations are less prepared. Organizations responsible for electrical, fuel, gas, energy, waste and water utilities ranked number one with lowest preparedness level. The findings of this study may help identify vulnerabilities and strategies to improve the resiliency of these critical infrastructures and institutions and may provide the basis to improve local policies pertaining to disaster preparedness.