Bolsonaro's lawyer Celso Vilardi confirmed his arrest but did not give a reason for the detention.
A person familiar with the matter said it was a preventative measure related to the terms of Bolsonaro's house arrest.
A federal police representative said Bolsonaro was undergoing intake exams in Brasilia on Saturday morning.
The former right-wing leader was sentenced in September to 27 years and three months in prison for plotting a coup to remain in power after losing the 2022 election to leftist President Luiz Inacio Lula da Silva.
Bolsonaro was identified as the leader and main beneficiary of a scheme to prevent Lula from taking office in 2023.
However, the courts have still not issued a final arrest order in that case, as Bolsonaro has not exhausted the appeals process.
For more than 100 days, Bolsonaro has been under strict house arrest for violating precautionary measures in a separate case over allegedly courting US interference to halt the criminal case against him.
US President Donald Trump, who was friendly with Bolsonaro when they were both in office, has called the case a "witch hunt".
He imposed sanctions on Moraes, the justice overseeing it, and a 50 per cent tariff on US imports of several Brazilian goods, which he began to roll back in November.
While under house arrest, Bolsonaro was barred from using social media, but received visits from political allies.
His defence is expected to seek permission for him to serve his sentence under house arrest, citing several health issues.
The former president, who was stabbed in the abdomen during a 2018 campaign event, has a history of hospitalisations and surgeries related to the attack.
Bolsonaro had previously been banned from running for office until 2030 after Brazil's electoral court found him guilty of abusing his office during his 2022 re-election campaign.
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