The facility has been the scene of gruesome violence between two rival gangs since the weekend, when 26 inmates were massacred
Elite officers entered the Alcacuz prison near the northern city of Natal to start the process, AFP journalists saw.
The facility has been the scene of gruesome violence between two rival gangs since the weekend, when 26 inmates were massacred, most of them beheaded.
"We are going to carry out this transfer as carefully as possible, respecting all security issues," a spokesman for the state police, local mayor Eduardo Franco, told reporters.
Four buses were brought in to take away prisoners who were members of one of the gangs. Three of the buses arrived with inmates from other facilities that were to be put in the vacated cells.
Wives and girlfriends of some of the prisoners being taken away tried to block the road but were dispersed when police fired rubber bullets.
The prisoner transfer underlined the tinderbox climate within Brazil's prison system, in which 134 people have been killed in prison violence this year according to the Folha de Sao Paulo newspaper, citing justice ministry figures.
Authorities are accused of long having allowed gangs to run the jails, which are filled well beyond their intended capacity.
In a bid to wrest back control, the government on Wednesday said it was deploying 1,000 troops to "clean out" arms, explosives and cellphones from various cellblocks in the country.
Defense Minister Raul Jungmann, who called the situation a "national emergency," said the soldiers "will only enter when the risk of rioting is minimal or nonexistent.... The armed forces are not going to confront these groups."
The troops, who include teams used during last year's Olympic Games in Rio, don't have the constitutional authority to take control of the prisons, only to confiscate dangerous contraband items.
Brazilian police had stormed the Alcacuz prison early Sunday to halt the bloodbath, but were still not in full control three days later.
Inside, the situation remained volatile as inmates from the rival drug gangs, the Sao Paulo-based First Capital Command (PCC), the country's biggest drug-trafficking group, and the Rio de Janeiro-based Red Command, squared off across a 50-meter (-yard) courtyard.
Officers had entered the facility earlier Wednesday -- amid inmates lighting fires and chanting -- with the aim of keeping the two sides separate while the transfer operation was prepared.
"We want those from the PCC to go to another state," an inmate had told AFP by telephone earlier. "We won't rest until (the authorities) take them away from here."
The uprising was tied to a turf war over control of cocaine trafficking within Brazil.
The rise of gang violence in the prisons and the increasingly tough measures to quell it raised anxiety in the public of a return to organized criminal action in Brazilian cities in towns.
A repeat of a May 2006 offensive by the PCC in Sao Paulo, the economic heart of the country, was especially feared.
Over three days, the gang launched some 200 attacks on police stations and cars, resulting in 90 deaths.
The subsequent ripple of terror triggered school, public transport and office closures, leaving the streets of the metropolis nearly deserted.
Other, more disparate and smaller attacks followed. In all, more than 500 people were killed, including police officers, PCC members and bystanders.
"The government has always acts when the horse has already bolted. It left the prisons in the hands of organized criminals," he said.
Brazil has the fourth biggest prison population in the world, with 622,000 inmates.