The blaze broke out in the morning in the machine room that houses the energy generators of the Comandante Ferraz station, the navy said in an emailed statement.
Two navy officials at the base died and a third was injured in the fire, Brazilian President Dilma Rousseff's office said in a statement. Rousseff's office said the base will be reconstructed.
The navy statement said that 44 people at the station at the time of the fire were transferred to Chile's Eduardo Frei station.
In a second statement, the navy said efforts to extinguish the fire were suspended because of bad weather. The firefighting crew was evacuated to the Chilean base and will return once the weather improves.
Chile's Defense Minister Andres Allamand told reporters the fire had "completely destroyed" the base. O Estado de S. Paulo quoted an unnamed official of the Brazilian navy saying the same thing.
A navy spokesman said those reports were "unfounded" and that as soon as the weather improves "we will evaluate the damage the fire caused to the station's structure."
The spokesman declined to be identified because he was not authorized to speak on the matter.
Separately, he confirmed a report posted Saturday on the O Estado de S. Paulo newspaper's website that a barge carrying diesel oil to the station sank during a storm in December.
According to the newspaper, the barge was carrying 2,640 gallons (10,000 liters) of diesel in its storage tank when it capsized and sank some 3,000 feet (900 meters) from Comandante Ferraz.
No one was on the barge as it was being towed by four small vessels from Brazilian navy ships to the base, which started operations in 1984.
So far, none of the fuel has leaked and two ships are expected to reach the site in about a week to try to bring the barge to the surface before any leaks occur, the newspaper said without revealing how it obtained the information.
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