It was the country's first new case of the disease formally known as bovine spongiform encephalopathy (BSE) since November.
Officials at the Health and Agriculture Ministry said on Sunday an eight-year-old Holstein cow from Kanagawa Prefecture, near Tokyo, had tested positive for BSE. It said the cow would be incinerated.
IMasako Kurimoto, director of the Agriculture Ministry's Animal Health and Animal Safety Division, said authorities were trying to learn the birth place of the cow.
"We are investigating ... how the cow finally ended up there," Kurimoto said. "It is also very important to find out what the cow was eating."
There have been no reports of people in Japan being affected by the human form of BSE, Creuzfeldt-Jakob Disease, which has killed about 130 people in Europe.
But Japan's food industry has been hard hit, especially after a ban was placed on the imports of US beef products in December after the first BSE case in the United States.
The United States has been trying to convince Japan, formerly the top foreign buyer of US beef, to resume imports.
But Japan has said it wants all US cattle tested for the disease, a demand the US cattle industry has rejected.