The workers will perform essential services and the decision will remain in effect until the strike is resolved, the reports said.
Issuing the order, Judge Jose Gutemberg de Barros Filho said the allegation that the strike was illegal was "plausible in principle."
The decision is expected to reduce the time taken to process environmental licenses for infrastructure and other projects under the government's US$250bn growth acceleration plan (PAC).
One of the government's concerns is that the strike could affect construction of hydroelectric power plants on the Madeira river.
Ibama employees are protesting the government's decision to split the regulator in two. The government's plan is for Ibama to continue to handle environmental fiscal policy and licensing but decisions on biodiversity and conservation to be made by the newly created Chico Mendes Institute.
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