Health Ministry officials and experts from a ministry panel on the disease were holding an emergency meeting to determine whether the man had contracted the disease by eating infected beef.
Masahito Yamada, a panel expert, said it was likely the man contracted the disease while living for one month in Britain — where mad cow first surfaced — in 1989.
"We believe it is highly likely that he contracted the disease during his visit to Britain," Yamada told reporters. "We cannot rule out the possibility that he ate the infected parts at that time."
Tetsuyuki Kitamoto, the panel's head and a professor of medicine at Tohoku University, said authorities would also have to investigate the possibility he was infected in Japan.
The human variant of Creutzfeldt-Jacob Disease has an incubation period of 10 years or more. A positive diagnosis often does not occur until the patient dies.
The ministry said the man first began to show signs of the disease in late 2001, when he was in his 40s. He became bedridden, unable to move or talk, and died in December.
It also said the man, who was not identified for privacy reasons, had no history of blood transfusions — another way the disease can be transmitted.
Ministry officials consulted with British experts last year and initially ruled out mad cow but continued to follow the man's condition.
There is no blood test to screen for the human form of the disease, nor is there a known cure or immunization.
But the Health Ministry stressed in a statement that, under normal circumstances, the disease is not transmitted between humans, and there was little worry of secondary infections.
The government's top spokesman also sought to reassure the public.
"While it is necessary to investigate the cause of the infection and possibility of secondary infection, this disease is not contagious. The Health Ministry will conduct a thorough investigation and also make sure that the public is properly informed," Chief Cabinet Secretary Hiroyuki Hosoda told reporters Friday evening.
Human infections have only been confirmed or deemed probable in 167 other people worldwide, virtually all of them in Britain but also in France, the United States, Ireland, Italy and Canada — though hundreds of thousands of people have likely eaten contaminated beef products.
Mad cow has spread through Europe and Asia since it was found in Britain. A fatal human form of the disease is believed to come from eating beef products from infected cows, especially tissue close to the animal's nervous system.
Since it was first discovered in Japan in 2001, 15 animals have been found with the disease — known formally as bovine spongiform encephalopathy, or BSE — but there have been no human cases.
Tokyo has checked every slaughtered cow before it entered the food supply since finding the first infected animal. The latest suspected case was found in October.
The government's spokesman, Hosoda, tried to ease worries that Friday's confirmation of the human mad cow case could hamper efforts by the United States to persuade Japan to ease its ongoing ban on U.S. beef imports.
"Japan and the United States are negotiating on the basis of scientific consultations," he said. "Future examinations will reflect that."
Japan banned American beef imports in December 2003 after the discovery of the first U.S. case of mad cow disease in Washington state. At the time, Japan was the most lucrative overseas market for American beef, with sales exceeding $1.7 billion in 2003.
The two sides tentatively agreed late last year to resume imports of beef products from cows younger than 21 months old but later stalled over differences about how to authenticate the age of cattle.