The justice minister indicated the gory violence may also have been a smokescreen for gang leaders to escape.
As police were engaged a huge manhunt for 126 escaped convicts still at large, Justice Minister Alexandre de Moraes suggested there may be more than meets the eye to the headline-grabbing prison riot.
"There was an escape plan already in place. So we need to investigate whether in reality all the unrest and the deaths happened so that (drug gang) leaders could escape," he said at a press conference in Brasilia.
Amazonas state officials say fighting between rival gangs triggered the riot, which lasted 17 hours and ended Monday morning with 56 inmates dead, many of them beheaded.
But the justice minister indicated the gory violence may also have been a smokescreen for gang leaders to escape.
The Amazonas state government had reinforced security at the Anisio Jobim Penitentiary Complex after being informed of a possible escape, he said.
Local officials did not tell federal authorities about the risk, he added.
A network of 16 tunnels was discovered at the prison in the wake of the riot, according to state public security secretary Sergio Fontes.
Officials say 112 inmates escaped through them. Another 72 escaped from the nearby Antonio Trindade Penal Institute.
Investigators meanwhile continued working to identify the bodies of inmates killed in the riot. They warn it could take weeks because many were badly mutilated.
As of Tuesday evening, 36 had been identified. Half the victims were beheaded, according to forensic investigators. Others were burned or dismembered.
The riot was the deadliest to hit Brazil's chronically overcrowded jails since police killed 111 inmates in a crackdown on an uprising at the Carandiru prison in Sao Paulo in 1992.
Amazonas authorities blame the riot on fighting between the powerful local gang Family of the North (FDN) and rivals from the First Capital Command (PCC), one of Brazil's largest gangs.