On Monday, Bolsonaro described the travel ban as an attempt to intimidate him, insisting he had no plans to leave Brazil.
The US State Department has said it would issue visas to defeated Brazilian presidential candidate Flavio Bolsonaro and his family following his loss to President Luiz Inácio Lula da Silva in Sunday's runoff election.
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A US official, speaking on condition of anonymity due to visa privacy laws, said “the State Department will issue visas to Flavio Bolsonaro and his family and allow them entry into the United States.”
However, Bolsonaro's whereabouts remain unclear, with conflicting reports about his movements after leaving Brazil despite a court order banning him from travelling abroad.
Argentine authorities said on Wednesday that the 45-year-old had entered Argentina "with valid travel documents and no legal impediment."
The country's migration agency said Bolsonaro travelled with his wife and two daughters aboard "a private flight operated by the company Baires Fly S.A. bound for the city of Guayaquil, Ecuador."
The same plane Argentine athorities said was carrying Bolsonaro then made a brief stop in Ecuador before reportedly flying to an unknown destination.
Earlier, US media outlets CNN and The Washington Post had reported that Bolsonaro arrived in the United States on Tuesday, citing anonymous sources. His reported arrival location was not disclosed.
Why is Bolsonaro fleeing Brazil?
Bolsonaro, who received tacit support from US President Donald Trump, is under investigation in Brazil for alleged corruption, money laundering and tax evasion.
He was ordered to surrender his passport and is expected to lose his parliamentary immunity following his election defeat.
Bolsonaro has maintained close ties with US President Donald Trump, whom he visited at the White House in May.
Trump, who did not formally endorse Bolsonaro in the runoff against Lula, said on Wednesday that he would welcome him to the United States, describing him and his family as "fine people".
"The election was really strange, and I thought it was terrible," Trump told reporters.