Bolsonaro has been taken into custody after authorities determined he posed a serious risk of fleeing while under home confinement.
The one-time leader was sentenced of planning a government overthrow in September and given more than 27 years in prison, but he remained under confinement pending legal challenges.
Top Judicial Official the presiding justice said the decision to arrest the 70-year-old politician was a safety action after fresh information emerged.
This encompassed attempting to break his electronic bracelet and a invitation to a public vigil that could "allow for a chance to flee".
In a paperwork permitting the custody, the magistrate said intelligence from the centre monitoring the former president's confinement suggested the one-time head of state's "intention to break the tracking monitor to ensure success in his flight.
This, it said, would be "facilitated by the chaos caused by the protest called by his son.
His son, Flávio, who works as a congressional representative, called for a assembly of his backers near Bolsonaro's home to take place on Saturday night.
The senator wrote on digital networks on the previous day: Do you plan to struggle for your homeland, or watch it all from your phone there on your couch? I invite you to fight with us."
He said the vigil would be so supporters could seek divine intervention for his physical condition and for the restoration of democratic rule in our country."
Part of the magistrate's ruling was the chance of Bolsonaro's transfer to foreign missions near the home, considering that the probes revealed a record of organizing to ask for protection through a consular facility", a announcement said.
The court filing emphasizes that the American diplomatic mission in the capital, the capital city, is located around 13km from the former president's residence.
Bolsonaro's legal woes have generated frustration from fellow populist conservative United States President President Trump, leading him to enact a fifty percent tax on Brazilian product imports.
The former president is being held in a federal law enforcement building in Brazil's capital city and will undergo a custody hearing on the following day.
It was only on last Friday that the ex-leader's attorneys asked the Top Court to authorize him to complete his entire prison term under house arrest, with electronic monitoring.
They also asked that the former president be allowed to exit his dwelling for healthcare, saying he demanded ongoing care for respiratory ailments and other illnesses.
Bolsonaro was found guilty of orchestrating a conspiracy aimed at keeping him in power after he was defeated in the 2022 election to his political opponent, President Lula.
Top judicial officials said that he knew of a plan which included plans to kill his opponent and his VP candidate, Alckmin, and to arrest and execute Justice Moraes - the Supreme Court justice who has been presiding over Bolsonaro's trial.
The plot was prevented because it failed to get the backing of the army and air force commanders. His successor was sworn in without problem on the first day of 2023.
But a seven days after, on January 8th, thousands of his backers stormed and vandalised official structures in the national capital, Brasília.
The security forces took action and around 1,500 people were taken into custody.
The justices found that the rioters had been incited by the former president whose scheme, they said, was for the country's army to take action, bring back stability and return him to office.
At the time, Bolsonaro's lawyers called the 27 years and three months sentence "absurdly excessive.
He was also banned from seeking elected position until twenty-sixty - eight years later after the completion of his term.
The ex-leader called the trial a targeted investigation" and said it was designed to prevent him running in the 2026 national vote.
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