The Amazonas state prison agency said all 42 prisoners found dead in Manaus on Monday showed signs of asphyxia.
The killings across the city's prisons recalled early 2017 when more than 120 inmates died at the hands of other prisoners during several weeks of fighting among rival crime gang members at prisons in northern states. Many of those victims had their heads cut off or their hearts and intestines ripped out.
On Sunday, 15 inmates were killed during a riot at Manaus' Anisio Jobim Prison Complex, where 56 prisoners died in the violence two years earlier.
Local authorities said prisoners began fighting among themselves before noon Sunday, and security reinforcements were rushed in and managed to regain control within 45 minutes.
Little information was released about Monday's killings.
Brazil's justice and public security ministry said it was sending a federal task force to help local officials handle the situation.
"I just spoke with (Justice) Minister Sergio Moro, who is already sending a prison intervention team to the State of Amazonas, so that he can help us in this moment of crisis and a problem that is national: the problem of prisons," Amazonas state Gov. Wilson Lima said.
Several drug-trafficking and other criminal gangs in Brazil run much of their day-to-day business from prisons, where they often have wide sway. The 2017 slayings were largely gang-related, prompting authorities to increase efforts to separate factions and frequently transfer prisoners.
Authorities have not yet said whether gang wars were behind the latest blood-letting.
Moro had to send a federal task force to help tame violence in Ceara state in January that local officials said was ordered by crime gang leaders angered by plans to impose tighter controls in the state's prisons.