FNS officers sealed off access to the Vila do Joao and Vila dos Pinheiros areas of the sprawling Complexo da Mare slum here on Thursday, reports Efe.
The two neighbourhoods are dominated by heavily armed drug gangs.
Besides the blockades, the FNS mounted a high-profile operation aimed at capturing the drug dealers who opened fire on three force members on Wednesday night.
One of the officers received a bullet wound to the head and remains in serious condition.
The FNS was assisted in the search by soldiers, Federal Police and members of local law enforcement.
"Two of the attackers were already identified and we will strive to arrest them as quickly as possible," Brazilian Justice Minister Alexandre de Moraes said.
The three FNS officers wondered into Vila do Joao by mistake, as were misdirected by a mobile app en route to downtown Rio de Janeiro.
The main highway linking Rio's airport with the area containing most of the Olympic venues crosses Complexo da Mare.
Nobody was hurt when a bullet struck one of the stables at the Olympic equestrian centre on Wednesday.
Last Saturday, a bullet fired from a long gun went through the roof of the press room at the equestrian centre, located in Rio de Janeiro's Deodoro neighbourhood.
The weekend incident was attributed to an attempt by a shooter in a nearby shantytown to hit one of the camera-equipped blimps that provide footage for Olympic television coverage.
A bus carrying journalists between Olympic venues was pelted with stones on Tuesday.
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