Ubiratan Guimaraes was killed Sunday in his apartment by unknown gunmen. Guimaraes was shot in the chest, said police investigators, who noted there was no sign of a struggle in the chief's apartment.
Guimaraes was convicted in 2001 for using excessive force to quell a 1992 prison riot that left 111 prisoners dead. The conviction was overturned earlier this year.
Police said they suspected that Guimaraes was killed by one of Brazil's notoriously violent criminal gangs.
Brazil's largest criminal gang, the First Capital Command, was formed in the wake of the Carandiru prison riot.