WASHINGTON—Supreme Court Justice Sonia Sotomayor on Monday publicly criticized a federal prosecutor for what she called "a racially charged remark" during a drug trial.

The comment came as the Supreme Court refused to hear an appeal of Bongani Charles Calhoun, who said during his 2011 trial he didn't know a group of men he was with at a hotel were preparing for a drug deal.

Assistant U.S. Attorney Sam Ponder asked him in open court, "You've got African Americans, you've got Hispanics, you've got a bag full of money. Does that tell you—a light bulb doesn't go off in your head and say, 'This is a drug deal?'"

Calhoun was convicted and sentenced to prison on drug conspiracy and firearm charges. He appealed his conviction, but the 5th U.S. Circuit Court of Appeals refused to overturn the convictions and sentence.

Sotomayor agreed with the decision not to hear the case, but said in a statement that she wanted to be sure that denial wasn't thought to "signal our tolerance of a federal prosecutor's racially charged remark."

Sotomayor criticized the prosecutor, saying the statement was "pernicious in its attempt to substitute racial stereotypes for evidence, and racial prejudice for reason. It is deeply disappointing to see a representative of the United States resort to this base tactic more than a decade into the 21st century."

"By suggesting that race should play a role in establishing a defendant's criminal intent, the prosecutor here tapped a deep and sorry vein of racial prejudice that has run through the history of criminal justice in our nation," she said, in a statement along with Justice Stephen Breyer.

She closed with: "I hope never to see a case like this again."