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The death toll rose to 57 from 46 while confirmed cases rose to 2,433 from 2,201 the day before.
Bolsonaro has aligned himself with U.S. President Donald Trump in prioritizing the economy over the shutdowns favoured by public health experts - including his own health minister Luiz Henrique Mandetta - who have warned the outbreak in Brazil could trigger a collapse of the healthcare system next month.
"Other viruses have killed many more than this one and there wasn't all this commotion," Bolsonaro told journalists. "What a few mayors and governors are doing is a crime. They're destroying Brazil."
As his boss downplayed the virus, national security adviser Augusto Heleno on Wednesday (local time) ignored medical advice to self-isolate for two weeks, instead returning to work just seven days into his quarantine after a positive coronavirus test. Heleno also attended cabinet meetings on the day he was waiting for the test result, Reuters learned.
In opposing shutdowns in Brazil's biggest cities and states, Bolsonaro has cast himself against local officials, congressional leadership, in addition to his health minister.
On Tuesday night, he played down the threat of the virus, assuring Brazilians that "90% of us will have no symptoms if contaminated" and his "history as an athlete" meant he personally would suffer at most "a little flu."
Senate President Davi Alcolumbre denounced his speech and called for "leadership that is serious, responsible and committed to the life and health of its people."
Sao Paulo Governor Joao Doria took Bolsonaro to task for not setting an example for Brazilians and appealed for him to "lead the nation, not divide it" at a time of crisis.
Two sources told Reuters that Bolsonaro's prepared 5-minute speech had been drafted without consulting health minister Mandetta.
The two have been at odds since Bolsonaro flouted guidelines and physically greeted supporters on March 15.
The country's top medical associations issued statements in support of Mandetta's approach to dealing with the epidemic, amid fears that the minister might resign from the job.
At a news conference on Wednesday, Mandetta, who denied that he was quitting, stressed the gravity of the epidemic and the need to keep up the drive to isolate the population from the virus.
Demand for electricity, a strong indicator of economic activity, fell sharply at the start of the week in Brazil, according to the National Electricity System Operator.
The agricultural sector, a powerhouse of the Brazilian economy, also said it was suffering due to the coronavirus, with farm lobby CNA warning that grain, coffee and sugarcane growers were facing operational hurdles.
Still, the Economy Ministry said it will not sacrifice long-term debt targets in order to rescue the economy. An official said there was no capacity for huge fiscal packages to fight the coronavirus crisis.
Economic Policy Secretary Adolfo Sachsida said any additional measures would only apply for this year, but warned that fiscal stability in coming years cannot be put at risk by overspending in 2020.
The government is struggling to transport medical equipment due to widespread flight cancellations, health minister Mandetta said, forcing authorities to rely on ground transportation.
Mandetta said the ministry would allow doctors to use the anti-malarial drug chloroquine to treat coronavirus.
The drug, described by Trump as a potential "game changer," has not yet been proven effective against the new coronavirus. A lead doctor on clinical trials in Brazil for the related drug hydroxychloroquine told Reuters that initial results would only be available in two weeks.