Outbreak management in disaster has to be planned and implemented prior to, during and after the disaster is over. The risk of outbreaks following disaster is related to the size, health status and living conditions of the displaced population. The risk is increased due standing water in floods for vector borne diseases, overcrowding, inadequate water and sanitation and poor access to health care. The 2006-2007 flood in Johore resulted in 2 episodes of food poisoning and an outbreak of coxsackie A24 acute haemorrhagic conjunctivitis. Only 19,667 (12.5%) of the 157,018 displaced persons suffered from communicable diseases which comprised of acute respiratory disease 7361(28%), skin infection 4241(19%), acute gastroenteritis 1872(8%) and conjunctivitis 589 (2%). The routine disease surveillance and environmental control were enhanced to cover the relief centers and flood areas. Risk assessment of communicable disease carried out resulted in prompt control measures and good coverage of preventive activities. In conclusion the Johore State Health Department has successfully manage the outbreaks during the major flood.