More than 60 people from the city's sanitation department have been working daily to remove the thousands of fish and will keep doing so until the problem is resolved, department officials said.
Specialists say the problem is caused by a rise in algae blooms. The situation occurs when the water contains too many nutrients and CO2 builds up and stops the fish from breathing.
"There was a big effort to stop sewage and we removed everything possible," Paulo Rosman, an oceanographer who has worked at the lagoon for years, told Reuters.
"But reducing the sewage doesn't mean you have reduced the algae blooms. That happens because of the excess of nutrients in the water."
Rosman said successive state and city governments have ignored proposals to improve water quality by dredging canals that lead into the sea.
The unfortunate situation on the banks of the Lagoa Rodrigo de Freitas is not new as tons of dead fish have appeared at regular intervals for decades.
The lagoon, one of Rio de Janeiro's picture postcard settings, is scheduled to stage canoeing and rowing events at the 2016 Olympics.
Water quality has been a major concern for organisers and the Guanabara Bay where the Olympic sailing events will be held has also being criticised.
The Rio de Janeiro state government promised to reduce the amount of raw sewage flowing into the bay by 80 percent but has since admitted that goal is unlikely to be met.
(Reporting by Andrew Downie in Sao Paulo, editing by Ed Osmond)
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