Judge Carlos Eduardo Martins said he had decided to suspend the project of 11 billion USD because it will hurt fishing activities on the Xingu River, where the dam should be built.
On Thursday the decision was posted on the website of the court.
Norte Energia consortium, responsible for the Belo Monte dam project, said he was not informed of the decision, which will probably be appealed.
If built, the dam will be the third largest producer of hydroelectric power in the world. The government says it will provide a clean, renewable energy, but environmentalists fear that the project promotes the construction of other dams in the Amazon, adding to deforestation in the region.