In a strategic escalation created to save his remaining term in power, Temer said that Janot availed himself of "deductions" to accuse him without proof and insinuated that the prosecutor had received money from a former aide.
What happens now? Under Brazilian law, the lower house of Congress must now vote on whether to allow the top tribunal to try the conservative leader.
Temer has denied wrongdoing and said the tapes were tampered with.
Supporters of Mr Temer say they have between 250 and 300 votes in the 513 seat parliament - enough to block a trial.
Prosecutors claim the money was an instalment on a 38 million reais (€10 million) bribe for Mr Temer from billionaire businessman Joseley Batista, whose family company J&F controls JBS, the world's largest meat-packer.
He also found time to accuse former Federal Prosecutor Marcelo Muller, a former aide to Rodrigo Janot, of leaving the Attorney-General's office without observing a quarantine period.
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Apart from Temer, one-third of his cabinet and four former presidents in the country have already been indicted or charged in different graft cases.
Brazil's President Michel Temer on Tuesday made an official statement to defend himself against the accusations of corruption that had formally presented by the Chief Prosecution Office.
Secondly, Temer reportedly told that same JBS leader to keep bribing someone else, and that was revealed thanks to a secretly recorded conversation. Lawmakers, particularly members of Temer's coalition, then spent several weeks soul-searching about whether to stick with the president or bail on him because of fears that association could be toxic for election chances next year.
According to documents filed at the Supreme Court, Temer is accused of corruption and obstruction of justice.
In that scenario, the current House Speaker Rodrigo Maia would assume the presidency.
Temer is also under investigation for obstruction of justice and belonging to a criminal organization.
The president's battle for political survival now centres on Brazil's lower house of congress.
Janot, however, is piling on the pressure and by separating the charges he would make sure that the crisis dragged on, weakening Temer's political base and making two thirds congressional approval for his trial more likely. "In that case, there will be defections, and colleagues may start to move against Temer". "Lawmakers are unwilling to jump the Temer government's ship when there is no clear ship to jump to".