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4 year oldMr Bolsonaro has clashed in recent weeks with state governors who have imposed lockdowns, denouncing the measures as "dictatorial".
As of Sunday, Brazil had more than 38,000 confirmed cases, the highest number in Latin America.
More than 2,400 people there have died.
President Bolsonaro addressed a crowd of a few hundred supporters outside army headquarters in the capital, Brasilia, on Sunday.
He said the protesters were "patriots" for defending individual freedoms.
As well as demanding an end to the lockdown, some of those attending the rally also held up signs calling for Brazil's Congress and the Supreme Court to be closed down.
Others said they wanted the military to take over the handling of the coronavirus crisis.
Brazil was under military rule for more than two decades from 1964 until 1985 and calls for the armed forces to be given more power are highly controversial.
While the president did not make any reference to those demands at the time, his appearance at the rally - at which people were calling for the closure of the country's democratic institutions - was labelled "provocative" by his critics.
On Monday, however, while talking to journalists, Mr Bolsonaro quickly responded to one of his supporters who called for the closure of the Supreme Court by stating that Brazil was a democratic country. He said that the nation's top court, as well as Congress, would remain open.
Journalists have noted that at Sunday's rally the president neither wore a face mask, even though he coughed on occasion, nor gloves - precautions which many other politicians in the region are taking.
He has in the past dismissed coronavirus as "little more than a flu".
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Rodrigo Maia, the speaker of Brazil's Chamber of Deputies and a critic of Mr Bolsonaro, tweeted that "the whole world is united against coronavirus, but in Brazil we have to fight the coronavirus and the virus of authoritarianism".
"In the name of the Chamber of Deputies, I reject any and all acts which defend the dictatorship," he added.
Relations between the president on the one hand and Congress and the Supreme Court on the other have been tense, with Mr Bolsonaro claiming they are trying to curtail his powers and even oust him.
Last week, the president sacked his health minister, Luiz Henrique Mandetta, who had backed the lockdown measures.
President Bolsonaro argues that the lockdown measures are damaging the economy and has argued that they should be eased and Brazil's borders reopened.
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