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The horn-honking protests took place Saturday in Rio de Janeiro, Sao Paulo and the capital of Brasilia and involved hundreds of people in trucks, cars and motorcycles.
Protesters demanded the resignations of governors over measures that have forced most businesses to close for weeks.
Bolsonaro has been a fierce critic of the states' stay-at-home measures, arguing that the economic harm could be more damaging than the illness.
On Friday, Bolsonaro fired his health minister, Luiz Henrique Mandetta, who supported the restrictions to contain the spread of the coronavirus.
Brazil, with a population of 211 million, has the most confirmed COVID-19 cases in Latin America — more than 36,500 — and at least 2,347 deaths. The outbreak’s peak is expected to hit Brazil in May.
In Rio de Janeiro, about 100 vehicles took part in the gridlock, cruising down Atlantica Avenue, along the iconic and temporarily shut down Copacabana Beach, according to Al Jazeera.
"Either we just have the pandemic, which is already a lot, or we have the pandemic and chaos," said state lawmaker Anderson Moraes, the news outlet reported. "For sure, lives are more important than anything else, but we can't take decisions today without thinking about tomorrow. Because tomorrow, I don't know how a family man will be when he sees his children going hungry."
In Brasilia, Bolsonaro reiterated his intention to start reopening the economy.
"The fear was excessive," he said on Saturday, denouncing the "greed" of politicians "who have shut down everything and created panic."
"People want a return to normality," the president said in a Facebook Live session shortly before meeting with a small crowd of supporters who had gathered outside the Planalto presidential palace. "We're going to start adding more flexibility."
The Associated Press contributed to this report.