Heavily-armed soldiers arrived in armored vehicles and trucks to help "pacify" the area between Rocinha and the upscale Gavea neighborhood, city security officials said.
Soldiers supporting local police searched for weapons and drugs in places where there had been gang clashes, or were local informants or intelligence units told them they could find the illegal goods, an adviser to the Rio state security office told AFP.
The soldiers were using equipment such as metal detectors "to sweep the area," the official said. "These are actions that must count with a surprise factor."
Military officials did not say how many soldiers were deployed in the Wednesday operation. Some 500 soldiers were sent on a similar operation on Tuesday.
Rocinha, a dense cluster of small homes on hillsides overlooking wealthy western Rio, is Brazil's most populous favela.
Violence is common in favelas, where around a quarter of Rio's population of 6.5 million live. Drug gangs control much of the territory and police are forced to remain on permanent alert.
The Rocinha power struggle reportedly pits supporters of Antonio Francisco "Nem" Bonfim, who used to control crime in the favela but has been in prison since 2011, and his wayward successor, Rogerio Avelino da Silva.
Bonfim's wife, Danubia de Souza Rangel, was arrested late on Tuesday in a favela near the Rio international airport, the police announced.
De Souza, sentenced last year to 28 years prison for drug trafficking, was a fugitive who taunted police by posting pictures of herself in bikini on social media.
At least nine people have been killed in the past days due to gang violence.
Some 3,000 students at Rocinha schools were told again stay home on Wednesday due to the violence. Stray bullets from gun battles can hit random civilians, and are known to land far from the fighting.
Security in Rio has declined steadily since last year's Olympic Games.
Wednesday's operation comes after 950 troops were sent to Rocinha in September to back police after heavily armed drug traffickers rampaged through the favela.
The troops left the favela on September 29, when officials declared the situation "stabilized."
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