The justices rejected a plea from the 5th U.S. Circuit Court of Appeals to rule on whether too much time had elapsed for the case against James Ford Seale to go forward.
The action leaves in place a lower court ruling that the statute of limitations had not expired for a federal kidnapping charge against Seale in the 1964 disappearance of two 19-year-old friends.
Seale was convicted in 2007 of abducting the men. Authorities said they were beaten, weighted down and thrown, possibly still alive, into a Mississippi River backwater.
Disagreeing with their colleagues, Justices John Paul Stevens and Antonin Scalia said the high court should have agreed to hear the case because it raises an important issue that potentially affects similar prosecutions. The court did not otherwise elaborate on its order.
The request by the New Orleans-based appeals court indicated that the decision could affect roughly two dozen other investigations into Civil Rights Era crimes. But Chief Judge Edith H. Jones and five other dissenters cast doubt on that number.
In 1964, when the men disappeared, kidnapping was punishable by death under federal law. But in the 1970s, Supreme Court decisions and acts of Congress changed the maximum sentence for kidnapping to life in prison. Capital crimes have no deadline for prosecution, but lesser crimes must be prosecuted within five years.
The question was whether the case should be decided under the law as it existed in 1964 or the stricter deadline that applies today.
Seale was serving life sentences in the 2007 conviction when a 5th Circuit three-judge panel ruled that the statute of limitations had passed and threw out his conviction.
The full 5th Circuit split 9-9, a vote that left in place the original finding by a Mississippi federal judge that the statute of limitations had not expired.
Prosecutors said Seale was with a group of Klansmen when they abducted Charles Eddie Moore and Henry Hezekiah Dee in southwest Mississippi. They took the teens into the woods and beat and interrogated them about rumors that blacks in the area were planning an armed uprising, prosecutors said.
The teens' remains were found in July 1964, when federal authorities searched for the bodies of three civil rights workers who had also disappeared that summer. The case of the three civil rights workers became known as "Mississippi Burning" and overshadowed the deaths of Dee and Moore.
Seale and another man, Charles Marcus Edwards, briefly faced state murder charges in the deaths of Dee and Moore. Prosecutors say the charges were dropped because local law enforcement officers were in collusion with the Klan.
Many people thought Seale was dead until 2005, when he was discovered living in a town not far from where the teens were abducted and the case was reopened.
Even after the high court's action, Seale has other issues on appeal.
The Supreme Court typically hears appeals submitted by the losing side in the lower courts. But the court does allow the appeals courts themselves to ask the justices to resolve nettlesome questions of law. The justices have agreed to hear cases in this way just four times in more than 60 years and not at all since 1981.
The case is U.S. v. Seale, 09-166.