Past major flooding events for the state of Johore, Malaysia were recorded in 1926, 1967, 1968 and 1971. However, major meteorological phenomena that hit Johore on the 19th December 2006 (first wave) and the 12th January 2007 (second wave) were claimed to be the worst flood disaster in Johore in a 100 years. All eight districts were affected displacing 157,018 and 155,368 population during the first and the second wave event respectively. The Johore Health Department deployed substantial number of medical and health personnel to deal with the Johore flood crisis. Flood-related data were collected on daily basis between 19th December 2006 and 19th February 2007 using spreadsheet format from Flood Operational Rooms located at respective District Health Offices. Among flood victims 34,530 were found to have non-communicable diseases and 19,670 with communicable diseases. No major food- and water-borne disease outbreaks, such as cholera and typhoid, were reported in Johore. High success of public health measures was depending on the workforce of medical and health personnel on the ground. On the other hand, voluntary services offered by non-governmental organisations (NGOs), private sector and other volunteers should be well coordinated without compromising regulatory and ethical requirements. Crisis guidelines and plan of actions shall be updated so that they would be more relevant to the crises encountered on the ground.