State officials said on Wednesday 93 followers of the Capital First Command gang - know as the PCC – had been killed since the violence erupted on Friday.
The authorities did not say who was killed, where or in what circumstances, leading to criticism from human rights groups.
Ariel de Castro Alves, coordinator of Brazil's National Human Rights Movement, said: "The climate of terror can't be turned into carte blanche to kill."
Newspapers used headlines such as "On the fifth day, revenge" and "Police respond with a massacre in Sao Paulo" in their reports on the police reaction.
About 40 police officers and four members of the public have been killed in the clashes and 18 inmates have died in prison uprisings blamed on the PCC.
The gangs launched a series of attacks on police stations, bars and banks in response to the transfers of their members, including leader Marcos "Marcola" Cacho, to a new high security prison.
Police said they believed PCC leaders were organising the violence from their cells using mobile phones and shut down transmitters near the prisons.
The PCC is the biggest criminal gang in Sao Paulo state and has a major power base in state prisons.
It has been blamed for a number of deadly jail riots in recent years.