A farm in central Japan saw 80 pigs die last week after catching the highly-contagious disease, an agricultural ministry official told AFP.
Early tests showed negative results for classical swine fever, as the illness is officially known.
But follow-up tests came out positive Sunday, prompting the cull of all 610 pigs at the farm, he added.
'Unprecedented' rain strands at least 1,000, kills at least 66 in Japan
"We are now processing the livestock there and disinfecting the farm," he said, adding that officials had set up sterilisation points on access roads to the affected farm.
The government has set up a team of specialists to analyse possible infection routes, the agricultural ministry said in a statement.
Tokyo halted pork exports after the outbreak was confirmed. The nation sold roughly $9 million in raw pork meat to foreign markets last year.
Japan saw its last case of classic swine fever, which does not affect humans, in 1992.
The disease continues to rage in many parts of Asia, Europe and Latin America.
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ