Bolsonaro has been taken into custody after authorities determined he posed a definite escape threat while under domestic detention.
The former head of state was sentenced of orchestrating a government overthrow in last fall and handed more than a 27-year term in incarceration, but he was staying under house arrest pending legal challenges.
Top Judicial Official Justice Moraes said the move to detain the elderly politician was a precautionary step after fresh information emerged.
This included trying to remove his ankle monitor and a invitation to a public vigil that could "allow for a possible escape.
In a filing authorising the arrest, the judge said data from the centre monitoring Bolsonaro's house arrest suggested the former leader's plan to remove the surveillance device to ensure success in his getaway".
This, it said, would be assisted by the confusion caused by the demonstration called by his offspring.
His child, Flávio, who works as a legislator, called for a meeting of his backers near the former president's residence to take place on the weekend.
Flávio Bolsonaro wrote on digital networks on last Friday: "Are you going to fight for your nation, or watch it all from your phone there on your sofa? I urge you to fight with us."
He said the gathering would be so followers could "pray for his health and for the restoration of democratic rule in our land."
Part of Justice Moraes's decision was the chance of Bolsonaro's transfer to foreign missions near the home, considering that the inquiries revealed a background of planning to ask for protection through a consular facility", a declaration said.
The legal document underscores that the United States embassy in the federal district, Brasilia, is located around 8 miles from his dwelling.
His judicial problems have provoked anger from fellow populist conservative American leader Donald Trump, causing him to implement a fifty percent tax on goods coming from Brazil.
Bolsonaro is being held in a federal law enforcement building in Brazil's capital city and will have a custody hearing on the next day.
It was only on last Friday that the his legal team asked the Top Court to authorize him to serve his whole jail sentence under home confinement, with digital surveillance.
They also asked that Bolsonaro be allowed to exit his dwelling for medical treatment, saying he demanded ongoing care for respiratory ailments and other ailments.
The former president was found guilty of heading a scheme aimed at maintaining his control after he failed to win the national vote to his left-wing rival, Lula.
Supreme Court justices said that he was aware of a scheme which encompassed plans to kill the current president and his running partner, his vice-presidential candidate, and to imprison and murder Justice Moraes - the High Court judge who has been presiding over his judicial proceedings.
The scheme was stopped because it failed to get the endorsement of the armed forces officials. The current president was sworn in without issue on 1 January 2023.
But a seven days after, on 8 January, thousands of his backers attacked and damaged 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 encouraged by him whose strategy, they said, was for the Brazilian military to intervene, reestablish control and bring him back to power.
At the moment, his attorneys called the decades-long sentence unreasonably severe".
He was also banned from seeking elected position until the year 2060 - eight years after the end of his sentence.
The ex-leader called the court case a "witch hunt and said it was intended to stop him participating in the next presidential race.
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