A total of approximately 3,000 patients have been recognized in the three prefectures of Kumamoto, Kagoshima and Niigata.

Recognition as a Minamata disease patient is given under the Act on Compensation, etc. for Pollution-Related Health Damage. As of the end of October 2021, there have been 2,999 recognized Minamata disease patients (1,790 in Kumamoto, 493 in Kagoshima and 716 in Niigata), among which 397 patients are alive (213 in Kumamoto, 71 in Kagoshima and 113 in Niigata).

In addition, there is a comprehensive medical aid program for those who are not recognized as patients but meet certain conditions, including affliction with a sensory disorder and high consumption of fish and shellfish. There are 38,320 recipients under this program (this total is in the three prefectures of Kumamoto, Kagoshima and Niigata).

The companies as well as the national government and Kumamoto Prefecture have provided compensation for the patients and work on the restoration of the polluted environment, among other actions.

The companies responsible for Minamata disease, Shin-Nippon Chisso Hiryo K.K. and Showa Denko K.K., are liable to compensate the patients, restore the polluted environment and provide compensation for fishing lost due to the pollution (the "polluter-pays" principle). Following a Supreme Court decision rendered in 2004 in the case known as the Minamata disease Kansai lawsuit, the national government and Kumamoto Prefecture were also found liable for damages.
With respect to Chisso Corporation, the national and prefectural governments have been providing financial support since 1978 by issuing prefectural bonds, due to the concerns that the company might become unable to pay these costs any longer.

Compensation includes damages for pain and suffering and coverage of medical expenses.

Once recognized as a patient under the Act on Compensation, etc. for Pollution-Related Health Damage, the patient will, pursuant to the agreement made with the responsible company, receive a lump-sum payment in damages for pain and suffering, as well as other payments, including a pension, medical expenses, medical allowances and nursing care expenses.
Pursuant to a politial solution reached in 1995, a recognized patient will receive a lump-sum payment from the polluting company and will also have a medical care handbook (changed name from "care handbook") issued under the comprehensive Minamata disease healthcare program, under which the patient may have payments for patient-payable portions of medical expenses, etc. covered by the national and prefectural governments. Those who are not eligible to have a medical handbook issued but have certain neurological symptoms will have a health handbook issued and have patient-payable portions of medical expenses, etc. paid for.

In addition, the Act on Special Measures for Aid of Minamata Disease Patient and Settlement of Minamata Disease Issues (Act No. 81 of 2009; hereinafter referred to as the "Minamata Disease Special Measures Act") was enacted in July 2009 and was then promulgated and came into force. Subsequently, a cabinet decision was made in April 2010 on the Policy for Aid Measures under the Minamata Disease Special Measures Act" (hereinafter referred to as "Aid Measures Policy"). Pursuant to this Aid Measures Policy, those who meet certain requirements will receive a lump-sum payment from the polluting company and will also, under the comprehensive Minamata disease healthcare program, have a Minamata disease victim handbook issued and have patient-payable portions of medical expenses covered by the national and prefectural governments and receive medical treatment allowance, etc. Those who do not meet the requirements mentioned above but are found to have certain neurological symptoms will have a Minamata disease victim handbook issued and have patient-payable portions of medical expenses, etc. paid for.

A large number of lawsuits have been filed, some of which are still in litigation.

In the court actions in which the polluting company was sued, in Niigata (1971) and in Kumamoto (1973), respectively, judgments were given in favor of the plaintiffs (patients). Since then, more than 10 cases have been brought before court.

Following a political solution reached in 1995 so as to solve the issue of Minamata disease, most of these cases had been withdrawn, but new actions were brought again after a Supreme Court decision came out in 2004 on the so-called Minamata disease Kansai case. As a result of discussions for settlement with some of the groups contesting in these actions that were held after the enactment of the Minamata Disease Special Measures Act in 2009, a settlement was reached in March 2011. There still are cases in litigation, however.