The announcement came days after President Luiz Inacio Lula da Silva complained about delays in the construction of two large hydropower dams in the Amazon.
Politicians and businessmen also have criticized what they view as slowness on the part of the agency -- known as Ibama -- in granting permits.
"Ibama will take care exclusively of supervision, licensing and authorization relating to the environment," Environment Minister Marina da Silva, a former rain forest activist, told a news conference.
A new agency called the Institute of Biodiversity will take over Ibama's conservation tasks.
Planned power projects, including two dams along the Madeira River in the western Amazon, have been delayed by the long process of getting environmental licenses.
Energy analysts say that as a result, Brazil is at high risk of energy rationing as early as 2010, which could harm the whole economy.
Conservationists seeking to protect the endangered Amazon, the world's largest rain forest, say they fear the government will try to ram through its development plans.
Last week Lula complained that studies on catfish had held up the dam projects.
Even if the government manages to cut through the environmental red tape, it may be just one of several steps needed to fast-track energy and transportation projects.
Brazil's complex judicial system and concerns over Indian rights also have long been sticking points for new projects.