The need for effective cooperation between the Veterinary and Fisheries Authorities in the field of aquatic animal health is widely accepted in Sri Lanka. International organisations have requested Sri Lanka to develop a model to promote this cooperation. With no tradition of aquaculture, Sri Lanka ventured into commercial aquaculture only a few decades ago. Epizootic ulcerative syndrome (EUS), monodon baculovirus and white spot syndrome virus are the only OIE recognized diseases reported. Responsibility for disease diagnosis, the implementation of preventive and control measures and certification is held by three institutions: the National Aquaculture Development Authority (NAQDA), the National Aquatic Research and Development Agency (NARA) and the Department of Animal Production and Health (DAPH). The National Centre for Disease Diagnosis and Health Management in Aquaculture is at the University of Peradeniya. The Fisheries and Aquatic Resources Act (No.2 of 1996), the Animal Diseases Act (No. 59 of 1992), the Animal Feeds Act of 1986 and the Aquaculture Management (Disease Control) Regulations 2000 provide the legislative framework for aquatic health issues. Coordination among the institutions involved in aquatic health management is inadequate and there is no proper policy and strategy for promoting aquatic health. Surveillance programs and epidemiological studies are also inadequate. A new structure has been proposed for better coordination between Veterinary and Fisheries Authorities in Sri Lanka to encourage all stakeholders in aquatic health control to participate in a coordinated effort. This new initiative will not only promote cooperation between Veterinary and Fisheries authorities but also strengthen the national aquatic animal health network.