Al Jazeera's Gabriel Elizondo said the jet crossed a busy road before hitting the fuel storage warehouse.
Dozens of ambulances raced to the crash site just outside the airport and television images showed the Airbus A320's tail sticking out from a building in flames as hundreds of firefighters tried to put out the blaze.
Hundreds of firefighters were trying
to put out the blaze [AFP]
The government said the body of one man was removed from the crash site. It gave no word on other fatalities or injuries.
Elizondo said an airline spokesman said there were employees inside the warehouse but could not say how many.
Brazil's Globo News television said at least six people were taken to the hospital.
The airport has been closed to air traffic and all streets around Congonhas airport - the largest domestic hub in the country - have been closed by police.