Police fired rubber bullets and tear gas canisters into the yard of the Alcacuz prison in northeastern Brazil as helicopters buzzed overhead.
Prisoners erected makeshift barricades, while inmates traded blows with wooden clubs and hurled stones.
Some police officers appeared to be firing live rounds from a watchtower.
There was no immediate word on deaths, but several inmates clearly appeared to be injured.
The outbreaks of violence were the latest in Brazil’s beleaguered penitentiary system, where 140 people have died in clashes in recent weeks.
The overcrowded prisons are now the battleground in a quickly escalating war between the nation’s two biggest drug gangs, the Sao Paulo-based First Capital Command (PCC) and the Red Command based in Rio de Janeiro.
For two decades, the two factions have maintained a working relationship, ensuring a steady flow of drugs and arms over Brazil’s porous border.
But about six months ago, the PCC began trying to muscle the Red Command out of drug routes.
The PCC has aggressively moved into new areas in the north and northeast of Brazil, where all the deadly clashes have taken place in recent weeks.
In response, the Red Command has allied itself with local gangs, enlisting them to take on the PCC.
The bloodshed has mostly played out inside the prisons, but security experts fear it will soon spill into already violent city streets.
The violence, the deadliest outbreak in the sharply criticised penal system in over two decades, has gripped Brazil.
Cellphone videos circulate widely on social media, some showing gang members chopping the heads off their rivals, slicing their hearts out and disemboweling them.
Members of a SWAT team entered the Alcacuz prison on Wednesday night to transfer more than 200 of the prisoners that belong to the “Crime Union of RN” gang – RN being initials for the local Rio Grande do Norte state, whose members had been killed this past weekend by PCC inmates.
Police said they searched cells and confiscated a large quantity of guns, knives, homemade weapons and bullet-resistant vests.
Caio Bezerra, the top security official for Rio Grande do Norte, told reporters that the Wednesday night operation was successful and that prisoners did not resist.
The spokesman for the state police force, Major Eduardo Franco, told Reuters late on Wednesday that the prison was back under control.
The killings began on January 1, when the powerful North Family gang, which is allied with the Red Command, killed 56 inmates at a prison in Amazonas state, mostly PCC members.
The North Family controls a lucrative cocaine route along the Solimoes, a branch of the Amazon that flows from Colombia and Peru, the world’s top two cocaine-producing nations.
The PCC retaliated on January 6 by killing 33 inmates at the Monte Cristo prison in the Amazonian state of Roraima, before carrying out the most recent killings at Alcacuz this past weekend.
In another prison in northeastern Brazil yesterday, at least one inmate was killed when members of different gangs clashed, authorities said.
Prisoners fought, burnt mattresses and ripped down part of the roof in one of the blocks of the Caico prison, also in Rio Grande do Norte, before being suppressed by guards, a spokesperson for the state’s security secretariat said.
Five inmates were injured in the clashes.
