Brazilian officials said 38 people were arrested in the operation, which followed mounting insecurity in City of God and other favelas where drug traffickers armed with automatic rifles rule the streets.
Troops were deployed at dawn mostly to encircle City of God, blocking access roads, while heavily armed police entered in search of suspects. However, an AFP correspondent also saw soldiers inside the favela where they and police guarded the maze-like network of streets.
Security forces also seized drugs, guns and ammunition, said the Rio state security ministry.
At least three people were killed last week in shootouts between police and drug gangs in City of God, a sprawling neighborhood famous for the 2002 movie of the same name.
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And on Tuesday in the Mare favela, there were fierce exchanges of gunfire between traffickers and police that left a 13-year-old boy dead.
Protesting locals set fires and used stones to block Rio's three principal highways, which all pass by Mare.
Some 1.5 million people live in Rio's favelas, or slums -- a quarter of the city's population.
Brazil's armed forces deployed to Rio de Janeiro in July 2017 to help the badly overstretched police. Rio state has been badly hit by Brazil's recession and the slump in the oil market in the last few years, as well as massive corruption.
Last month, Defense Minister Raul Jungmann said that nationwide the security system "is broken."
The Rio carnival gets into full swing on Sunday, with the colorful samba parades attracting an estimated 1.5 million tourists.
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