Supreme Court Justice Sonia Sotomayor arrives for the presidential inauguration on the West Front of the U.S. Capitol January 21, 2013 in Washington, D.C. (Pool/Reuters)

Supreme Court Justice Sonia Sotomayor accused a Texas federal prosecutor Monday of tapping into a “deep and sorry vein of racial prejudice” in his questioning of a black man facing a drug charge.

The justices did not accept Bongani Charles Calhoun’s request that the court review his conviction, but Sotomayor appended a scathing statement to make sure that the court’s denial would not be seen as a signal of “tolerance of a federal prosecutor’s racially charged remark.”

Sotomayor did not name Assistant U.S. Attorney Sam L. Ponder in her statement, but she denounced his questioning of Calhoun, who maintained in court that he did not know that the friends with whom he was traveling were planning a drug deal.

Ponder had asked Calhoun: “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?’ ”

Sotomayor, who in 2009 became the court’s first Hispanic member, said Ponder’s question was “pernicious in its attempt to substitute racial stereotype for evidence, and racial prejudice for reason.”

She added: “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. Such conduct diminishes the dignity of our criminal justice system and undermines respect for the rule of law. We expect the government to seek justice, not to fan the flames of fear and prejudice.”

In an interview, Ponder said that “I can’t disagree with the idea she was expressing” and contended he “wasn’t trying to interject race” into the case.

Calhoun’s testimony was that he was merely getting a ride home from a road trip with the other men and was unaware that they were planning a drug deal. But he also said he had become nervous the night before when one friend had arrived at the hotel room with a bag of money.

Ponder said he was pressing Calhoun on what had made him nervous and why he could not have foreseen that a drug deal was in the offing.

“The question I was asking was about his state of mind,” Ponder said.

Asked if he had been criticized by his superiors for the line of questioning, Ponder said “that already happened” before the statement from Sotomayor.

Justice Stephen G. Breyer joined Sotomayor’s statement.

Sotomayor said she agreed with the rest of the court that technical mistakes by Calhoun’s trial attorney — “Inexplicably . . . Calhoun’s lawyer did not object to the question” — meant his petition should be denied. But she added, “I hope never to see a case like this again.”

Sotomayor’s statement came on a day when the court struggled to find a balance between society’s interest in bringing finality to criminal prosecutions and a defendant’s right to receive competent counsel or to present new evidence of innocence.

In a separate case, the court heard arguments about a claim of innocence made by a Michigan man, Floyd Perkins, who was sentenced to life in prison in 1993 for the gruesome murder of his friend Rodney Henderson.

Testimony showed Perkins had told someone else he intended to kill Henderson and later apologized for the murder. But at his trial, Perkins blamed the killing on a third man who was with them.

Without new evidence, Perkins had only a year under the law to make a federal claim that his attorney had inadequately assisted him. Perkins over the years gathered three affidavits — from his sister, a friend and a dry-cleaning clerk — that he said helped show his innocence. But he did not file his petition until five years after obtaining the third of those statements.

Michigan Solicitor General John J. Bursch told the court that a decision to allow Perkins to pursue his case now would open the floodgates to prisoners claiming to present new evidence.

A prisoner must be diligent in filing a petition because of the “compelling, countervailing state interest in having notice and an opportunity to investigate evidence as soon as it’s discovered.”

Trying to add to the skepticism of some justices about Perkins, Bursch said: “No one thinks that Mr. Perkins is actually innocent based on this new evidence — at best, it proves that he had a co-conspirator who helped him commit the murder together.”

Perkins’s attorney, Chad A. Readler, said the court’s ultimate concern must be whether a case presents a miscarriage of justice, not whether Perkins was negligent or delayed in making his claim.

“Diligence is not the ultimate equity — it’s innocence,” Readler said. “And if a petitioner can come forward and make a credible showing of actual innocence, that standing alone has always been enough to allow a federal court to at least go ahead and then reach the underlying claim.”

The case is McQuiggin v. Perkins.