The case of bovine spongiform encephalopathy was detected in an animal that died in 2010 in the southern state of Parana.
"The case poses no risk whatsoever to public health or to animal hygiene, since the animal did not die from the disease mentioned and was buried on the property," the agriculture ministry said in a statement.
"Brazil does not have cases of BSE."
Still Japan, a small importer of Brazilian meat, halted its imports, prompting Brazilian authorities to seek clarification.
"We received explanations from the (Brazilian) Agriculture Ministry and immediately relayed them to Tokyo," Kentaro Morita, a diplomat at the Japanese embassy in Brasilia, told AFP.
He added that the Japanese government was now "analyzing the situation" to determine the next steps.
The agriculture ministry launched a "preventive action" to preempt similar measures by key importers.
"We are in touch with countries to reaffirm that the atypical case of the disease carries no risk for exports," it added.
Authorities said the World Organization for Animal Health had been notified of the case and in response indicated it was "maintaining Brazil's status as a country with an insignificant risk of BSE, the best existing risk classification."
With nearly 200 million head of cattle, Brazil is the leading beef meat exporter and Russia its main customer.