Brazil declared an animal health emergency over avian flu in May after confirming multiple cases in wild birds, and reported its first outbreak of the disease among marine mammals last month in the state of Rio Grande do Sul.
The country, the world's biggest chicken exporter, has not reported any cases in domesticated birds or commercial poultry operations.
The Rio Grande do Sul agriculture department said the dead seals and sea lions had been found at various points along its coast.
Several of the animals were found near Brazil's border with Uruguay, which also recently reported hundreds of seals and sea lions killed by avian flu.
Peru, Chile and Argentina have also reported cases in marine animals.
Brazil remains classified as free of avian flu, as no cases have been detected in commercial poultry operations, according to the government.
The country supplies around 35 percent of all poultry on the international market.
"The notifications do not change the health situation in the state or the country, and there is no risk from consuming poultry or eggs," the Rio Grande do Sul agriculture department said in a statement.
There is no treatment for avian flu, which is often deadly in animals.
Avian influenza viruses do not typically infect humans, although there have been rare cases.
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