Bolsonaro has been arrested after authorities determined he posed a definite escape threat while under house arrest.
The former head of state was sentenced of planning a government overthrow in the ninth month and handed more than a 27-year term in incarceration, but he was staying under confinement pending legal challenges.
Top Judicial Official the presiding justice said the decision to arrest the 70-year-old politician was a precautionary step after "new facts" emerged.
This involved trying to remove his ankle monitor and a call for a demonstration that could enable a potential flight.
In a document approving the custody, the judge said intelligence from the facility tracking his home detention suggested the ex-president's "intention to break the tracking monitor to ensure success in his getaway".
This, it said, would be "facilitated by the disorder caused by the gathering called by his offspring.
His offspring, his son Flávio, who holds office as a senator, called for a meeting of his supporters near his father's house to take place on Saturday evening.
His son wrote on social media on Friday: "Are you going to fight for your homeland, or watch it all from your mobile device there on your sofa? I call on you to battle with us."
He said the gathering would be so supporters could offer prayers for his well-being and for the reestablishment of democratic governance in our country."
Part of the judge's decision was the possibility of the former president's move to foreign missions near the residence, considering that the probes revealed a history of planning to ask for protection through a diplomatic representation", a announcement said.
The court filing underscores that the United States embassy in the federal district, the capital city, is located around approximately 13 kilometers from his dwelling.
His judicial problems have provoked anger from fellow populist conservative US President President Trump, causing him to implement a 50% tariff on goods coming from Brazil.
He is being held in a national police facility in Brazil's capital city and will experience a custody hearing on Sunday.
It was only on last Friday that the former president's lawyers asked the Supreme Court to permit him to fulfill his full incarceration period under home confinement, with digital surveillance.
They also asked that he be authorized to leave his home for healthcare, saying he needed frequent medical attention for respiratory ailments and other ailments.
He was convicted of leading a conspiracy aimed at maintaining his control after he failed to win the national vote to his political opponent, President Lula.
High Court judges said that he knew of a plot which involved plans to kill Lula and his VP candidate, Alckmin, and to arrest and execute Justice Moraes - the Supreme Court justice who has been overseeing his judicial proceedings.
The conspiracy was prevented because it couldn't obtain the support of the military leaders. The current president was took office without issue on the first day of 2023.
But a week later, on 8 January, thousands of his followers invaded and destroyed official structures in the federal district, Brasília.
The police stepped in and around fifteen hundred individuals were arrested.
The judges found that the rioters had been provoked by him whose strategy, they said, was for the Brazilian military to step in, bring back stability and bring him back to power.
At the time, Bolsonaro's lawyers called the 27 years and three months sentence unreasonably severe".
He was also prohibited from seeking elected position until the year 2060 - eight years after the completion of his term.
The former president called the legal proceedings a "witch hunt and said it was aimed at blocking him running in the 2026 presidential election.
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