On 1 May, the hospital director reported to the local public health office the discovery of an "epidemic of an unknown disease of the central nervous system", marking the official discovery of Minamata disease.To investigate the epidemic, the city government and various medical practitioners formed the Strange Disease Countermeasures Committee at the end of May 1956. Owing to the localised nature of the disease, it was suspected to be contagious and as a precaution patients were isolated and their homes disinfected. Although contagion was later disproved, this initial response contributed to the stigmatisation and discrimination experienced by Minamata survivors from the local community. During its investigations, the committee uncovered surprising anecdotal evidence of the strange behaviour of cats and other wildlife in the areas surrounding patients homes. From around 1950 onward, cats had been seen to have convulsions, go mad, and die. Locals called it the "cat dancing disease", owing to their erratic movement. Crows had fallen from the sky, seaweed no longer grew on the sea bed, and fish floated dead on the surface of the sea. As the extent of the outbreak was understood, the committee invited researchers from Kumamoto University (or Kumadai) to help in the research effort.The Kumamoto University Research Group was formed on 24 August 1956. Researchers from the School of Medicine began visiting Minamata regularly and admitted patients to the university hospital for detailed examinations. A more complete picture of the symptoms exhibited by patients was gradually uncovered.
Some people feared the disease to be contagious, and many local people were fiercely loyal to Chisso, depending on the company for their livelihoods. In this atmosphere, those affected were reluctant to come forward and seek certification. Despite these factors, over 17,000 people have applied to the council for certification. Also, in recognising an applicant as having Minamata disease, the certification council qualified that patient to receive financial compensation from Chisso. For that reason, the council has always been under immense pressure to reject claimants and minimise the financial burden placed on Chisso. Rather than being a council of medical recognition, the decisions of the council were always affected by the economic and political factors surrounding Minamata and the Chisso corporation. Furthermore, compensation of the victims led to continued strife in the community, including unfounded accusations that some of the people who sought compensation did not actually have the disease. More properly, the impact should be called a criminal poisoning, not a clinical disease. These forms of obfuscation are commonly experienced by environmental victims in many countries.In 1978, the National Institute for Minamata Disease was established in Minamata. It consists of four departments: The Department of Basic Medical Science, The Department of Clinical Medicine, The Department of Epidemiology and The Department of International Affairs and Environmental Sciences. In 1986, The Institute became a WHO Collaborating Centre for Studies on the Health Effects of Mercury Compounds.