Elite officers yesterday 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.
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.
Defence 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.
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