A count released by the authorities listed 49 injured people and seven detained in the protests.
In it, Temer is heard authorizing Bautista to pay millions in hush money to a convicted former politician who was aware of the prevalence of bribery and corruption in the highest levels of Brazilian government. The president has denied wrongdoing and said he will not resign.
The use of troops in the nation's capital is particularly fraught in Brazil, where many still remember the repression of the country's 1964-1985 military dictatorship.
Meirelles, a favorite of investors who took over the finance ministry a year ago and headed the central bank under Brazil's leftist former president, Luiz Inacio Lula da Silva, is seen as a prime contender to replace Temer.
Young lawmakers in the PSDB wanted to abandon his government immediately last week when the top court approved the corruption probe into Temer.
Demonstrations against his government turned violent on Wednesday, and he briefly deployed troops to contain protesters who demanded his resignation.
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Leaders from 29 nations, including Italy, Russia and Indonesia, were in attendance. Britain, France and Germany were represented by finance or trade officials.
In a decree published in the Official Diary, Temer revoked the order issued the previous day, saying that "the halt to acts of destruction and violence and the subsequent reestablishment of law and order" had motivated him to pull back the troops. The protest was largely peaceful until a group of masked members of the so-called black bloc, a group that has frequently been infiltrated by agent s provocateurs, attacked police and vandalized government ministry buildings, setting one, the agricultural ministry, on fire.
"It's unacceptable that judges should be pressured, but that doesn't stop legal arguments from the defense being presented in a robust way", he said. The weeklong deployment was authorized by a presidential decree that left open the possibility that soldiers could be used more widely in Brasilia.
Temer's popularity was low even before the latest scandal broke, in part because of opposition to an economic overhaul that he wants to push through Congress, including loosening work rules and changing the pension system.
According to Folha, the bourgeois parties that had backed Temer during the ouster of Rousseff are now banking on Brazil's Federal Superior Electoral Tribunal (TSE) issuing a ruling early next month invalidating the 2014 election of Rousseff and Temer, then her vice presidential running mate, on the grounds that the campaign was illegally financed.
Andre Cesar, a political analyst at Hold consultancy, said Temer "cannot survive". Renan Calheiros, who is the whip for Temer's party in the upper house but has increasingly challenged the president.
Associated Press photographer Eraldo Peres reported this story in Brasilia and AP writer Mauricio Savarese reported from Rio de Janeiro.
While Congress debated, 35,000 people were marching toward the legislative building, shouting "Out with Temer!" and carrying signs calling for an immediate direct presidential election.
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