Talking to journalists in Ribeirão Preto, in the interior of southeastern state of São Paulo, after visiting an ethanol plant Ban said he was aware of the controversy surrounding the biofuels movement.
"Some fear that land currently used to grow food will instead be turned over to fuel," he said. "Others worry that forests will be cut down to make way for biomass plantations. Still more worry about the effects on the environment and biodiversity."
National governments must take the lead in managing their use and ensuring that the benefits outweigh the costs, he said.
The Secretary-General described the ethanol plant he visited as "one of many green technologies that show promise in offsetting global warming and he commended both the Brazilian government and private business enterprises in Brazil for trying to develop clean and renewable sources of energy.
"Brazil is the quiet green giant. It leads the world in renewable energy. It has one of the cleanest energy economies in the world. Brazil is one of the few nations to successfully produce biofuels on a large scale," he said, calling for increased international attention to "what Brazil is achieving."
Ban travelled to the capital, Brasília, for talks and a working luncheon with the country's President, Luiz Inácio Lula da Silva.
Climate change has been the focus of the UN chief's trip as he has visited Argentina, Chile and then Antarctica, where he saw first-hand the effects of global warming on the continent's melting and diminishing glaciers.