The superintendent of the Pará Penitentiary System (Susipe) said that at least 52 inmates at the Altamira Regional Recovery Center were killed, 16 of whom were beheaded, the Efe news reported.
Several other people were injured and two prison officers were taken hostage before being released.
The confrontation began at 7 a.m. (local time), at breakfast, when members of a criminal organisation invaded the complex where members of a rival faction were held, according to Susipe's press office.
Prisoners then began fighting with handmade weapons, locked themselves in a room and set fire to the building.
The flames spread throughout the complex and a number of inmates died due to smoke inhalation.
Military and civil police went into the prison and managed to contain the uprising and negotiate the release of the hostages.
Susipe said that they have not yet identified the dead or the criminal organisations involved.
"We are conducting an inspection and counting the prisoners, so the number of dead and injured could still grow," a spokeswoman said.
Once the riot was controlled, the inmates involved in the attack were transferred to individual cells and isolated from the others.
There had not been any "information or signals" from intelligence services that indicated "a possible conflict" in the prison, according to Susipe.
The Altamira Regional Recovery Center, located about 850 kilometers from the regional capital of Pará, Belém, has the capacity for 200 prisoners, but currently houses 311 people.
This was the second largest massacre in a Brazilian jail so far in 2019.
In May, 55 inmates were killed in less than 48 hours in four prisons in the city of Manaus, also in northern Brazil, an occasion that sparked an intense debate about prison conditions in the country.
( With inputs from IANS )