At a deforestation conference on Thursday, scientists from Brazil's National Institute of Amazon Research said about 400 million tonnes of carbon dioxide were emitted in 2003.
The figure is 60% higher than previous estimates which had failed to take into account the amounts of gas released by rotting vegetation.
"Its emitting much more than it is absorbing," said Philip Fearnside, a researcher at the institute.
The conference is discussing the findings of the Large Scale Biosphere-Atmosphere Experiment in Amazonia, the world's biggest study of jungle deforestation. It started in 1998 and is being conducted by Brazilian and foreign organisations, including the US space agency NASA.
The Amazon, a continuous forest covering an area larger than the continental United States and home to up to 30% of the world's animal and plant species, lost 5.9 million acres to logging and burning in 2003.
Fearnside said hydroelectric dams in the Amazon, for instance, should be included in any analysis because rotting trees in flooded areas release methane gas. The Amazon's four dams produced more emissions between them than Brazil's largest city, Sao Paulo, he said.
But Carlos Nobre of Brazil's National Institute of Space Research disputed Fearnside's theory.
"His number is not believable," said Nobre, who estimated Amazon produced 250 million tones of carbon dioxide last year.
The issue is politically sensitive because Brazil is due to publish an inventory of its emissions this year as required by the Kyoto Protocol on global warming.
Scientists expect the inventory to give a figure of about 300 million tonnes for Brazil's total emissions, which would make the country one of the world's top 10 polluters.
But Fearnside's figure could tip it into the top five.