In patients, the maximum mercury level recorded was 705 parts per million (ppm), indicating very heavy exposure and in nonsymptomatic Minamata residents, the level was 191 ppm. This compared to an average level of 4 ppm for people living outside the Minamata area.On 12 November 1959, the Ministry of Health and Welfares Minamata Food Poisoning Subcommittee published its results:

Minamata disease is a poisoning disease that affects mainly the central nervous system and is caused by the consumption of large quantities of fish and shellfish living in Minamata Bay and its surroundings, the major causative agent being some sort of organic mercury compound. 1959
During the Kumadai investigation, the causal substance had been identified as a heavy metal and it was widely presumed that the Chisso factory was the source of the contamination. Chisso was coming under closer scrutiny and to deflect criticism, the wastewater output route was changed. Chisso knew of the environmental damage caused by its wastewater and was well aware that it was the prime suspect in the Minamata disease investigation. Despite this, from September 1958, instead of discharging its waste into Hyakken Harbour (the focus of investigation and source of original contamination), it discharged wastewater directly into Minamata River.
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.