Authorities said the Madureira, Mercadao and Otaviano stations were shut on Saturday after traffickers opened fire on a police car, Xinhua news agency reported.
The stations are part of the newly opened Transcarioca bus line, built for the upcoming Olympic Games slated to begin from August 5.
No injuries were reported from the exchange of fire and there were no arrests.
Authorities in Rio are battling to contain a rise in violent crime as the city prepares for the Olympic Games.
In the first five months of 2016, the number of murders in Rio rose by 18 per cent to 1,870 compared to the same period in 2012 when killings reached their lowest rates of the past decade.
Brazil will deploy 88,000 soldiers and police during the August 5-21 Games, more than double the number used at the London 2012 Olympics.
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