He ruled in favor of a fisheries group which argued that the Belo Monte dam would affect local fish stocks and could harm indigenous families who make a living from fishing.
The government says the dam is crucial to meeting growing energy needs.
Judge Martins barred the Norte Energia company behind the project from “building a port, using explosives, installing dikes, building canals and any other infrastructure work that would interfere with the natural flow of the Xingu river, thereby affecting local fish stocks”.
He said the building of canals and dikes could have negative repercussions for river communities living off small-scale fishing.
The judge said building work currently underway on accommodation blocks for the project’s many workers could continue as it would not interfere with the flow of the river.
The consortium behind the project is expected to appeal against the decision.
In June, the Brazilian environment agency backed the construction, dismissing concerns by environmentalists and indigenous groups who argue that it will harm the world’s largest tropical rainforest and displace tens of thousands of people.
The agency, Ibama, said the dam had been subjected to “robust analysis” of its impact on the environment.
The 11,000-megawatt dam would be the third biggest in the world – after the Three Gorges in China and Itaipu, which is jointly run by Brazil and Paraguay.
Judge Murdered
A senior Brazilian police officer has been arrested on suspicion of ordering the murder of a judge who investigated police corruption.
Lt Col Claudio Luiz de Oliveira was detained in Rio de Janeiro, and arrest orders have been issues for at least six other policemen in the city.
Prosecutors say Col Oliveira ordered the killing to cover up another murder that his officers were accused of.
Judge Patricia Acioli was shot 21 times as she was leaving her home in August.
She had made a name for herself with a tough stance on police corruption, handing out heavy sentences in a number of cases.
Hours before she was killed, she had issued arrest warrants for a group of officers under Col Oliveira’s command in connection with the death of an 18-year-old.
Diego Beliene died in a clash with police in Sao Gonçalo, a city across the bay from Rio. Police officers on the scene said the teenager had resisted arrest, but investigators have since said he may have been murdered.
Prosecutors say Col Oliveira was hoping to put an end to her investigation.
However, prosecutors do not believe he was aware that the judge had issued arrest warrants for some of his men over the teenager’s death.