Bolsonaro's son, Flavio Bolsonaro, has come under fire over suspicious payments to his former driver flagged by the Council for Financial Activities Control, the country's financial regulatory body.
The Bolsonaros and the driver deny wrongdoing over $320,000 that changed hands from 2016-2017 and came to light late last year.
The controversy deepened Thursday when a Supreme Court justice, Luiz Fux, ordered a Rio de Janeiro state court to temporarily suspend the probe.
Flavio Bolsonaro's lawyers argued that being a senator-elect means the case must be decided by the Supreme Court, a privilege enjoyed by politicians in Brazil. Flavio and other senators will be confirmed when Congress convenes next month.
"It's absurd," said Adriana Balthazar, a leader of "Come to the Streets," a conservative, anti-corruption group that organizes street protests and supported Bolsonaro during last year's campaign. "It's a horrible example from a government that I wanted to believe in. It's totally against everything the Bolsonaros preached in the campaign."
As candidates, Bolsonaro and his son ran on anti-corruption platforms and railed against such protections.
One of the flagged payments passed through the bank account of the president's wife, Michelle Bolsonaro.
However, even some supporters say their explanations have fallen flat. For example, the president explained the payment to his wife by saying it was repayment of a personal loan to the driver, and it went to the account of the future first lady because Bolsonaro himself was too busy to go to the bank.
While it's not clear what happened and no charges have been filed, one possibility is a scheme that is common in Brazilian politics. It works like this: a lawmaker hires several people on the condition of getting a kickback from their salaries. Before being elected to the Senate, Flavio was a state deputy in Rio de Janeiro.
The financial regulator has said that many of the payments to the driver, Fabricio Queiroz, came on pay days for people on Flavio Bolsonaro's payroll.
"There is no way to agree with this decision, which goes against the Supreme Court's own precedent," said Deltan Dallagnol, a lead prosecutor in Brazil's largest ever corruption investigation, Operation Car Wash.
Janaina Paschoal, a state deputy whose name was floated as a possible vice presidential pick for Bolsonaro, tweeted that the justice's decision was "erroneous."
Kim Kataguiri, a leader from another rightist street movement wrote that Flavio Bolsonaro's request, "has a bad smell," and was "at minimum, suspicious."
Local media reported growing discomfort among the military members of the administration, an influential force in Bolsonaro's government.
Old tweets and videos resurfaced of Bolsonaro and his son Flavio criticizing the legal immunity that kept sitting politicians from being brought to justice for corruption charges.
"The honeymoon could already be over with Bolsonaro" said Mauricio Santoro, a political scientist from the State University of Rio, referring to the high hopes Bolsonaro's voters have for ending Brazil's endemic corruption. "It's a big problem and the family is dealing with it the worst way possible," he said, referring to the Supreme Court request and the lack of concrete explanation.
Santoro said that beyond Bolsonaro's core base, many Brazilians who helped Bolsonaro win 55 percent of the vote in October did so principally because they saw a chance for a change from the old way of Brazilian politics.
"That part of the electorate will not be faithful if he proves to default to business-as-usual politics," Santoro said.