Temer, the first sitting president of Brazil to face criminal charges, is accused of accepting bribes from a giant meatpacking company.
He is also under investigation for obstruction of justice and belonging to a criminal organization.
If the lower house of Congress votes by a two-thirds majority to accept the charge, the center-right president would be suspended for 180 days and face trial in the Supreme Court.
However, Temer's aides say they are confident he has sufficient support in the scandal-plagued Congress -- where dozens of lawmakers have been caught up in the same sweeping graft probe targeting Temer -- to get the charge thrown out.
A source in the presidency, speaking on condition of anonymity, told AFP that Temer sees the charge lodged late yesterday by Prosecutor General Rodrigo Janot as flimsy.
"It was political. The charge is very weak and the president will fight it. He is angry and feeling combative because he considers this process absurd," said the source, who had recently met with Temer.
The presidency considers the task of securing at least one-third of the votes in the lower house to be "not the end of the world."
Temer's latest approval ratings are just seven percent, lower even than his leftist predecessor Dilma Rousseff, whom he replaced last year when she was impeached and removed from office by his congressional allies.
"Of course you could switch the political class with other people but the most corrupt ones in this whole affair would probably escape unharmed," said Nicolas Crapez, 34, on his way to work at the state government in Rio de Janeiro.
"We are no longer represented. The political parties have drifted away from their voters, from society's concerns."
Many lawmakers are themselves facing corruption investigations. Also, there is no agreement on a corruption- free consensus candidate who could fill Temer's shoes until scheduled elections in October 2018 if he were removed.
On the other hand, Janot appears set to deny Temer an opportunity to clear his name quickly, since the bribery charge is likely to be followed separately by others -- each one going to the lower house of Congress for a vote.
The bribery charge is linked to the arrest of a close former presidential aide caught carrying a suitcase stuffed with 500,000 reais (about USD 150,000) cash that prosecutors say was part of payments from JBS meatpacking executives to Temer.
Temer acted "in violation of his duties to the state and to society," Janot said, citing "abundant" proof of bribe taking.
Temer says that his former aide was acting independently and that there is nothing to link him to the suitcase. The aide is in detention facing corruption charges, but has so far refused to cooperate with prosecutors.
Batista secretly recorded Temer allegedly discussing the hush money and gave the recording to prosecutors in a plea bargain to secure leniency in his own corruption case.
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