The administration could seek a review by the full court when it reconvenes in February.

In a separate case, Mr. Temer’s administration is seeking to bar the imprisonment of people convicted of crimes until their appeals have been exhausted. In a brief before the Supreme Court, the executive branch has argued that delaying prison sentences safeguards defendants’ rights. Prosecutors counter that such a move would represent a return to an era in which white-collar cases languished for years during appeals.

“It would do great harm to Lava Jato in the best of cases, delaying the execution of sentences for at least a decade,” said Roberson Pozzobon, a prosecutor assigned to a Lava Jato task force in Curitiba, the southern city where the investigation began. “This setback would mean the institutionalization of impunity and would therefore create a great incentive for criminal practices, notably corruption.”

These debates are playing out amid an effort by some lawmakers to vastly reduce the number of officials shielded from prosecution in conventional courts. The protection, which was established by Brazil’s 1988 Constitution upon the re-establishment of democracy, gives privileged legal standing to about 55,000 officials.

“It served an important role in the country in the 1980s, at a time when there was fear that people would be prosecuted for their words and their deeds back when the justice system was weak,” said Representative Efraim Filho, who backs the effort to curb the protection. “Now it’s an anachronism that conveys a message of impunity, of privilege, of an elite that is entitled to a different treatment than ordinary citizens.”

The legal protection allowed Mr. Temer to avoid being prosecuted early this year after Ms. Dodge’s predecessor, Rodrigo Janot, filed two sets of charges against him.

Mr. Temer spent much of the year horse-trading with lawmakers, who twice voted to prevent the cases from being referred to the Supreme Court, the only court where senior officials may be prosecuted. Mr. Temer called Mr. Janot a headline-grabbing, overzealous prosecutor and expressed hope that Ms. Dodge would be more measured.

The president, who came to power after helping orchestrate the impeachment of President Dilma Rousseff last year, could still face charges when his term ends at the end of 2018. The newspaper O Globo reported in November that Mr. Temer’s allies had begun considering ways to extend his legal protection — for instance, by getting him appointed an ambassador.