This proposal split the members of the patients society, many of whom were extremely wary of entrusting their fate to a third party, as they had done in 1959 with unfortunate results. At a meeting on the 5 April 1969, the opposing views within the society could not be reconciled and the organisation split into the pro-arbitration group and the litigation group (who decided to sue the company). That summer, Chisso sent gifts to the families who opted for arbitration rather than litigation. An arbitration committee was duly set up by the Ministry of Health and Welfare on 25 April, but it took almost a year to draw up a draft compensation plan. A newspaper leak in March 1970 revealed that the committee would ask Chisso to pay only ¥2 million ($5,600) for dead patients and ¥140,000 to ¥200,000 ($390 to $560) per year to surviving patients. The arbitration group were dismayed by the sums on offer. They petitioned the committee, together with patients and supporters of the litigation group, for a fairer deal. The arbitration committee announced their compensation plan on 25 May in a disorderly session at the Ministry of Health and Welfare in Tokyo. Thirteen protesters were arrested. Instead of accepting the agreement as they had promised, the arbitration group asked for increases. The committee was forced to revise its plan and the patients waited inside the ministry building for two days while they did so. The final agreement was signed on 27 May.
Masazumi Harada has said that, "It may sound strange, but if this second Minamata disease had not broken out, the medical and social progress achieved by now in Kumamoto... would have been impossible. "Around this time, two other pollution-related diseases were also grabbing headlines in Japan. People with Yokkaichi asthma and itai-itai disease were forming citizens groups and filed lawsuits against the polluting companies in September 1967 and March 1968, respectively. As a group, these diseases came to be known as the four big pollution diseases of Japan.Slowly but surely, the mood in Minamata and Japan as a whole was shifting. Minamata patients found the public gradually becoming more receptive and sympathetic as the decade wore on. This culminated in 1968 with the establishment in Minamata of the Citizens Council for Minamata Disease Countermeasures, which was to become the chief citizens support group to the Minamata patients. A founding member of the citizens council was Michiko Ishimure, a local housewife and poet who later that year published Pure Land, Poisoned Sea: Our Minamata disease, a book of poetic essays that received national acclaim. 1969–1973
Official government recognition
Finally on 26 September 1968 – twelve years after the discovery of the disease (and four months after Chisso had stopped production of acetaldehyde using its mercury catalyst) – the Japanese government issued an official conclusion as to the cause of Minamata disease:

Minamata disease is a disease of the central nervous system, a poisoning caused by long-term consumption, in large amounts, of fish and shellfish from Minamata Bay.