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.
He also spoke of his opposition to the 1958 change in wastewater output route to Minamata River. Hosokawas testimony was backed up by a colleague who also told how Chisso officials had ordered them to halt their cat experiments in the autumn of 1959. Hosokawa died three months after giving his testimony. Former factory manager Eiichi Nishida admitted that the company put profits ahead of safety, resulting in dangerous working conditions and a lack of care with mercury. Former Chisso President Kiichi Yoshioka admitted that the company promoted a theory of dumped World War II explosives, though it knew it to be unfounded. The verdict handed down on 20 March 1973 represented a complete victory for the patients of the litigation group:

The defendants factory was a leading chemical plant with the most advanced technology and ... should have assured the safety of its wastewater. The defendant could have prevented the occurrence of Minamata disease or at least have kept it at a minimum. We cannot find that the defendant took any of the precautionary measures called for in this situation whatsoever. The presumption that the defendant had been negligent from beginning to end in discharging wastewater from its acetaldehyde plant is amply supported. The defendant cannot escape liability for negligence. The "sympathy money" agreement was found to be invalid and Chisso was ordered to make one-time payments of ¥18 million ($66,000) for each deceased patient and from ¥16 million to ¥18 million ($59,000 to $66,000) for each surviving patient.