Environmental protection agency Ibama estimated around 10,000 shortfin mako and blue sharks were killed to harvest the fins, which are considered a delicacy in Asia.
"It is possibly the largest seizure in history of this type of product," Ibama environmental protection director Jair Schmitt said in a statement.
The fins were seized from two export companies, one in the southern state of Santa Catarina, the other in the southeastern state of Sao Paulo, officials said.
Other firms are also being investigated, they added.
Shark fishing is banned in Brazil.
Officials said the companies had illegally used permits for other species to amass the huge haul.
Shark fin soup is believed by some in countries including China and Japan to have medicinal and aphrodisiac properties, though studies have not confirmed the claims.
The animal parts can fetch up to $1,000 a kilogram in Asia, according to the Wildlife Conservation Society.
The black-market shark fin trade is estimated to be worth $500 million a year.
Indiscriminate fishing is causing a "drastic reduction" in shark populations worldwide, said Ibama.
However, sharks got a boost in November, when 183 countries approved a plan to protect 54 species from the hammerhead and requiem shark families -- two of the most-trafficked for shark fin soup -- under the Convention on International Trade in Endangered Species (CITES).
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