Unrest spread to the town of Natal near the jail, prompting the government to order the armed forces to the town.
Police fired rubber bullets and tear gas to try to separate two groups of inmates as they fought a pitched battle in the courtyard of the Alcacuz prison, AFP reporters overlooking the facility saw.
Unrest also erupted overnight in the town of Natal near the jail, prompting the government to order the armed forces to deploy to the town.
"The troops will reinforce the patrols in the streets of Natal after the riot in Alcacuz prison," President Michel Temer's office said in a statement.
Globonews television channel showed pictures of injured inmates being evacuated from the jail.
Rioting had also broken out overnight in six towns in the state, a spokesman for local authorities told AFP.
Rioters set on fire 21 buses plus other vehicles and seven people were arrested in that unrest, the spokesman said.
One person died and five were hurt during another prisoner uprising in the nearby town of Caico, he said.
On Wednesday, elite officers entered the Alcacuz prison near the northern city of Natal and transferred 220 inmates to another jail.
In the town, groups allied with the imprisoned gang members "attacked buses in revenge for the decision to separate the prisoners," state governor Robinson Faria said.
"The situation got much worse last night."
The Alcacuz facility was the scene of gruesome violence between two rival gangs last weekend when 26 inmates were massacred, most of them beheaded.
That was the third major mass killing in a Brazilian prison this year.
So far this year 134 people have been killed in prison violence, according to the Folha de Sao Paulo newspaper, citing justice ministry figures.
Authorities are accused of allowing gangs to run the overcrowded jails.
Defense Minister Raul Jungmann called the situation a "national emergency."
Brazilian police had stormed the Alcacuz prison early Sunday to halt the bloodbath, but were still not in full control four days later.
Rival groups of prisoners remained loose in the courtyard, sheltering behind barricades of mattresses and furniture.
The prison was built for a maximum of 620 inmates but currently houses 1,083, the state justice department said.
Experts say the violence is part of a war between drug gangs battling for control of one of the world's most important cocaine markets and trafficking routes.
Brazil shares borders with Colombia, Bolivia and Peru, the world's three biggest cocaine producers. It is a key route for trafficking the drug to Europe.
At Alcacuz, inmates from the country's biggest gang, the Sao Paulo-based First Capital Command (PCC), faced off against allies of their rivals from the Rio de Janeiro-based Red Command.
The Natal massacre raised fears that the wave of violence could spread across the country -- including to the crime-plagued metropolis of Rio de Janeiro.
About 60 inmates were killed in the northwestern city of Manaus on January 1. Many were beheaded and mutilated.
A further 33 died in a prison riot in Roraima state on January 6.
After those two riots, Temer announced that the federal government would spend $250 million to build new prisons.