It came as inmates were removed from Alcacuz Prison in Natal city, where 26 people were killed on Sunday.
The inmates are said to have all been members of one gang.
After the estimated 220 prisoners left, police special forces searched the cells and found firearms, a bullet-proof jacket and a large quantity of knives, Caio Bezerra, Natal state`s security chief, told reporters.
Most of the unrest which has gripped Brazil`s overcrowded northern prisons is understood to stem from violence between the country`s two largest gangs - the Sao Paulo-based First Capital Command (PCC) drug gang and Rio de Janeiro`s Red Command.
At least 134 prisoners have been killed since the start of the year, Fohla de Sao Paulo newspaper reported. A large number of those killed were decapitated.
The defence minister described the situation as a "national emergency".
The troops do not have the authority to take control of the prisons, but will be used to "clean out" weapons, explosives and phones, Mr Jungmann said.
Police were forced to break up further violence at Alcacuz on Tuesday, when the gangs clashed once more.
On Wednesday, one inmate at the Natal prison told news agency AFP by telephone they wanted "those from the PCC to go to another state".
"We won`t rest until (the authorities) take them away from here," he added.
Four buses were later seen removing members of one of the rival gangs, while another three buses appeared to be waiting to bring in people to fill the vacated cells.
However, relatives unhappy with the transfer attempted to block the road.
Thirteen buses were destroyed, apparently as part of the protest.
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