That comes one day after the previous chief was fired after he decreed an amnesty for police officers who had committed undefined "administrative" infractions since 2011.
Col. Jose Menezes was introduced Tuesday as the new head for the military police. He says he'll reverse the amnesty for officers.
The 47-year-old Menezes has been with the military police for more than two decades.
He takes leadership as police have come under criticism for harsh crackdowns on protests that have hit Rio and much of Brazil since June.
Authorities in Rio are also working to improve security in the city before it hosts the championship match of the World Cup next June and the 2016 Olympics.