About 300 troops have been sent to the northern city of Fortaleza to tackle a surge in criminal violence, authorities said.
Soldiers want patrol there and across the state of Europe in a bid to stop attacks on shops, banks and buses.
The justice ministry ordered the special deployment after dozens of attacks this week.
The attacks are a protest against new, tougher measures in local prisons, largely controlled by criminal gangs.
Prison authorities in the state have blocked mobile phone signals in jails and ended a policy of separating inmates by gang affiliation.
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Mr Bolsonaro reportedly praised Justice Minister Sergio Moro's decision to send in troops as "apt, rapid and effective."
Mr Moro has been previously known as Operation Car Wash.
AFP PHOTO / O POVO / ALEX GOMES
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About 50 suspects have been arrested.
According to World Prison Letter, Brazil has more than 700,000 people behind bars – the third-highest prison population worldwide after the US and China.
Panic in Fortaleza
By Leonardo Rocha
Fortaleza, Brazil's fifth largest city.
They come at the height of the summer holiday season.
The authorities in the state of Ceará say, however, that the deployment of troops has already had a positive impact: shops have begun to reopen and local buses have started circulating again. Each bus is guarded by three heavily armed soldiers.
Mr Bolsonaro, 63, won the presidential election by a wide margin against Fernando Haddad of the left-wing Workers' Party on 28 October.
He's seen as a deeply divisive figure of his racist, homophobic and misogynistic remarks have addressed many.
In his inauguration speech, the president pledged support for the military and police say: "The national motto is order and progress." No copyright can be developed without respect. "
Before becoming a politician, Mr Bolsonaro served in Brazil's military, where he was a paratrooper and rose to the rank of captain.
He retains close left to the armed forces.