The finding does not mean the virus can be readily transmitted through the bodily fluids.
The main method of infection is via mosquito bites, but scientists are investigating all other possibilities.
While Zika infection is normally mild, it has been linked to thousands of suspected birth defects.
Traces of Zika have been detected in other bodily fluids in previous outbreaks, but the Brazilian authorities say this is the first time "active" virus has been detected.
Prof Jonathan Ball, a virologist at the University of Nottingham, told the BBC: "Because we can detect a virus in a particular body fluid it does not mean that it will become an important source of virus for transmission to humans.
"At the peak of virus replication in the blood, virus can often be detected in other body fluids, but the levels of virus are often much lower and there is no obvious or efficient means for the virus to get from that bodily fluid into another person`s bloodstream."
Active Zika found in saliva and urine
06 February 2016
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Active Zika virus has been detected in the saliva and urine of patients, the Brazilian government`s health institute says.
