As soon as these ringleaders are identified, at the request of the Manaus state government they will be transferred, said the minister, Alexandre de Moraes.
The riot broke out Sunday afternoon and lasted through the night at aprison on the outskirts of Manaus, the capital of Amazonas state, state public security secretary Sergio Fontes said.
Bloodied and burned bodies were seen stacked in a concrete prisonyard and piled in carts.
A total of 184 inmates escaped, and so far 40 have been caught, Moraes said.
The fighting ranks among the most deadly of numerous prison riots across Latin America in the past decade.
Fontes called it the biggest massacre ever committed at a prison in the state.
Outside, heavily armed police hunted for inmates who escaped through a series of tunnels discovered at the Anisio Jobim penitentiary complex.