The Tokyo District Court has rejected a civil lawsuit demanding that tests into food toxicity and illnesses required by law be carried out for "Minamata disease" poisoning.
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Doctor Toshihide Tsuda, who sued, said Wednesday he would appeal the court's decision.
Minamata disease, one of Japan's worst environmental disasters, refers to mercury poisoning from eating fish and shellfish.
Thousands of people were sickened or crippled from the mercury leaks by chemical company Chisso Corp., which continued for more than a decade.
Advocates on behalf of the victims have sought for 60 years to get laws requiring the tests to be carried out.
Tsuda contends there would have been far fewer victims if tests had been done right away, and even today can help identify them. Lawsuits for certification are still ongoing.