The incident was the latest involving water quality in the bay, where sailing, open water swimming, and triathlon races are due to take place at the Games in August.
"Officials found rubbish in the water and on the beach as well as a considerable number of dead fish all from the same species of sardine," the government's State Environmental Institute said in a statement.
"These fish because of their low commercial value are often thrown overboard by trawlers as we have seen on other occasions in this same area."
Other than floating garbage the officials saw no "visual abnormalities" in the water. They took samples and will report back in five days.
When Rio bid to host the 2016 Olympics, the city said it would cut the amount of raw sewage flowing into the bay by 80 percent but has since confirmed it will not meet that target.
An independent report last year found there were dangerously high levels of viruses and bacteria in the water.
(Reporting by Andrew Downie, editing by Ed Osmond)
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