When this produced no results, the alliance members took their campaign to Tokyo, securing an official visit to Minamata by members of the Japanese Diet. During the visit on 2 November, alliance members forced their way into the factory and rioted, causing many injuries and ¥10 million ($100,000) worth of damage. The violence was covered widely in the media, bringing the nations attention to the Minamata issue for the first time since the outbreak began. Another mediation committee was set up, and an agreement was hammered out and signed on 17 December. Some ¥25 million of "sympathy money" was paid to the alliance and a ¥65 million fishing recovery fund was established. In 1959, the people with  Minamata disease were in a much weaker position than the fishermen. The recently formed Minamata Disease Patients Families Mutual Aid Society was much more divided than the fishing cooperatives. Patients families were the victims of discrimination and ostracism from the local community. Local people felt that the company (and their city that depended upon it) was facing economic ruin. To some patients, this ostracism by the community represented a greater fear than the disease itself. After beginning a sit-in at the Chisso factory gates in November 1959, the patients asked Kumamoto Prefecture Governor Hirosaku Teramoto to include the patients request for compensation with the mediation that was ongoing with the prefectural fishing alliance. Chisso agreed and after a few weeks further negotiation, another "sympathy money" agreement was signed.
Payments for deaths ranged from ¥1.7 million to ¥4 million ($4,700 to $11,100), one-time payments from ¥1 million to ¥4.2 million ($2,760 to $11,660) and annual payments between ¥170,000 and ¥380,000 ($470 to $1,100) for surviving patients. On the day of the signing, the Minamata Citizens Council held a protest outside the Chisso factory gates. One of the Chisso trade unions held an eight-hour strike in protest at the poor treatment of the arbitration group by their own company.The litigation group, representing 41 certified patients (17 already deceased) in 28 families, submitted their suit against Chisso in the Kumamoto District Court on 14 June 1969. The leader of the group, Eizō Watanabe (a former leader of the Mutual Aid Society), declared, "Today, and from this day forth, we are fighting against the power of the state." Those who decided to sue the company came under fierce pressure to drop their lawsuits. One woman was visited personally by a Chisso executive and harassed by her neighbours. She was blackballed by the community, her familys fishing boat used without permission, their fishing nets were cut, and human faeces were thrown at her in the street.The litigation group and their lawyers were helped substantially by an informal national network of citizens groups that had sprung up around the country in 1969. The Associations to Indict those Responsible for Minamata Disease were instrumental in raising awareness and funds for the lawsuit. The Kumamoto branch, in particular, was especially helpful to the case.