Patients who were certified by a Ministry of Health and Welfare committee would be compensated: adult patients received ¥100,000 ($917) per year; children ¥30,000 ($275) per year, and families of dead patients would receive a one-off ¥320,000 ($2935) payment. Wastewater treatment
On 21 October 1959, Chisso was ordered by the Ministry of International Trade and Industry to switch back its wastewater drainage from the Minamata River to Hyakken Harbour and to speed up the installation of wastewater treatment systems at the factory. Chisso installed a Cyclator purification system on 19 December 1959, and opened it with a special ceremony. Chissos president Kiichi Yoshioka drank a glass of water supposedly treated through the Cyclator to demonstrate that it was safe. In fact, the wastewater from the factory, which the company knew still contained mercury and led to Minamata disease when fed to cats, was not being treated through the Cyclator at the time. Testimony at a later Niigata Minamata disease trial proved that Chisso knew the Cyclator to be completely ineffective: "The purification tank was installed as a social solution and did nothing to remove organic mercury. "The deception was successful and almost all parties involved in Minamata disease were duped into believing that the factorys wastewater had been made safe from December 1959 onward. This widespread assumption meant that doctors were not expecting new patients to appear, resulting in numerous problems in the years to follow as the pollution continued. In most peoples minds, the issue of Minamata disease had been resolved.
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.