Military police inspector general Sidney Camargo said the four men faced prosecution and expulsion after being identified by their alleged victims.
"The military police is outraged and will take all available measures to investigate these crimes; the officers involved will be dismissed" if found guilty, Camargo told the Globo television network.
The four officers were all members of a Police Pacification Unit (UPP), specially created police squads set up to restore law and order in Rio de Janeiro's crime-ridden slums.
The three victims filed a complaint yesterday against six police officers and underwent medical exams.
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Camargo, who condemned the attacks as "barbaric," said two other police officers had been placed on "administrative" detention.
Rio authorities launched the favela pacification program in 2008 in order to clean up the city's slums ahead of the World Cup and the 2016 Olympics.
There are currently 9,000 police officers deployed across 253 favelas as part of the pacification program, according to officials.