Bolsonaro has been detained after authorities concluded he posed a serious risk of fleeing while under house arrest.
The former head of state was found guilty of orchestrating a military coup in September and sentenced more than 27 years in incarceration, but he was staying under home detention pending court reviews.
Top Judicial Official Alexandre de Moraes said the decision to arrest the elderly politician was a precautionary step after "new facts" emerged.
This included trying to remove his tracking device and a invitation to a public vigil that could "allow for a possible escape.
In a paperwork permitting the arrest, Justice Moraes said intelligence from the facility tracking the former president's confinement suggested the ex-president's plan to remove the electronic ankle bracelet to guarantee victory in his escape.
This, it said, would be "facilitated by the disorder caused by the protest called by his son.
His son, Flávio, who works as a senator, called for a assembly of his followers near Bolsonaro's home to take place on Saturday evening.
The senator wrote on social media on last Friday: Will you battle for your homeland, or observe everything from your phone there on your sofa? I call on you to battle with us."
He said the gathering would be so followers could seek divine intervention for his health and for the restoration of democratic rule in our land."
Part of Justice Moraes's ruling was the potential of his move to diplomatic missions near the residence, considering that the inquiries revealed a background of organizing to request asylum through a consular facility", a declaration said.
The court filing emphasizes that the American diplomatic mission in the capital, the capital city, is located around approximately 13 kilometers from his dwelling.
His judicial problems have provoked anger from fellow populist conservative US President Donald Trump, prompting him to impose a half-rate duty on goods coming from Brazil.
The former president is being held in a national police facility in Brasilia and will undergo a detention review on the following day.
It was only on the previous day that the his legal team asked the Top Court to authorize him to complete his entire prison term under house arrest, with electronic monitoring.
They also petitioned that he be allowed to leave his home for healthcare, saying he required ongoing care for pulmonary infections and other illnesses.
Bolsonaro was determined responsible of leading a scheme aimed at keeping him in power after he failed to win the 2022 election to his political opponent, President Lula.
Supreme Court justices said that he knew of a plan which included plans to assassinate his opponent and his vice-presidential running mate, Alckmin, and to detain and kill Alexandre de Moraes - the Supreme Court justice who has been presiding over the former president's case.
The conspiracy was stopped because it didn't receive the support of the armed forces officials. His successor was took office without incident on January 1st, 2023.
But a following week, on the eighth of January, numerous Bolsonaro supporters invaded and destroyed public facilities in the capital, the capital city.
The security forces took action and around approximately 1,500 persons were arrested.
The judges found that the protesters had been incited by the former president whose scheme, they said, was for the country's army to intervene, reestablish control and reinstate his authority.
At the time, the legal team called the 27 years and three months sentence "absurdly excessive.
He was also banned from campaigning for office until the year 2060 - eight years after the end of his sentence.
The one-time head of state called the court case a targeted investigation" and said it was intended to stop him participating in the 2026 national vote.
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