The court rejected a last-ditch attempt by Temer to have his obstruction of justice and racketeering case suspended. A 6-0 majority on the court voted down Temer's appeal, with five more justices still due to vote.
That clears the way for the case to be considered by the lower house of Congress.
If the chamber of deputies votes by a two thirds majority in favour, Temer -- the first sitting Brazilian president to face criminal charges -- would have to stand down for 180 days and face trial at the Supreme Court.
The latest charges involve Temer's alleged agreement to pay hush money to keep a jailed politician from testifying and his leadership of a group in Congress that took millions of dollars in bribes from companies seeking state contracts.
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His lawyers attempted to put the case on hold, arguing before the Supreme Court that one of the main pieces of evidence in the prosecution -- plea deal testimony from a meatpacking tycoon -- needs to be reconsidered because of irregularities.
A review of the case might have suited Temer because the prosecutor general who brought the charges, Rodrigo Janot, stepped down at the end of last week. Janot was replaced by Raquel Dodge, whom analysts say may be less aggressive.
At issue now is testimony given by JBS meatpacking magnates Joesley and Wesley Batista, who confessed to conducting wide ranging bribery of politicians and testified against Temer.