The decision means the high court will not take the unusual step of short-circuiting appeals courts as they consider contrary opinions over the legitimacy of the agency's vast surveillance program.
Conservative lawyer Larry Klayman had persuaded a federal judge in December to rule that the agency's activities likely violate the Constitution's ban on unreasonable searches. The judge in Washington, D.C., put his decision on hold pending a government appeal.
The justices rejected without comment Klayman's long-shot request to bypass the appeals process and hear the case immediately. Klayman argued that the constitutional questions raised were too important to wait for the U.S. Court of Appeals for the D.C. Circuit to reach a decision. But the Supreme Court rarely grants such requests.
It could take many months before the justices consider any legal challenge to the controversial collection program disclosed by former NSA systems analyst Edward Snowden. Klayman's lawsuit is one of two dueling NSA cases currently winding their way through the federal appeals system.
Just days after Klayman won his case, a federal judge in New York reached the opposite conclusion in rejecting a similar challenge to the NSA program from the American Civil Liberties Union. U.S. District Judge William H. Pauley III validated the NSA operation as an effective "counterpunch" to terrorist acts.
Other legal challenges to the NSA program have yet to be decided. Sen. Rand Paul, R-Ky., and the conservative advocacy group FreedomWorks filed a federal lawsuit in February in Washington, D.C., seeking to have the phone records program declared unconstitutional. And a coalition of environmental groups, human rights activists and church leaders brought a similar challenge last year in San Francisco.
Klayman has said he made his push for a Supreme Court decision because he fears the Obama administration wants to have the New York case reviewed first, because it favours the government's position. Klayman contends the Justice Department is trying to stretch out the appeals process in his case. He says that the Supreme Court should not wait for the appeals process to play out, given the enormous consequences of the government's "outrageous intrusion of privacy" and the loss of constitutional freedoms.
The Justice Department declined a request for comment. The Obama administration has defended the NSA program as a crucial and effective tool against terrorism. The agency did not submit a brief to the Supreme Court responding Klayman's request to bypass the appeals process.
Earlier this year, President Barack Obama called for ending the government's control of Americans' phone data and immediately ordered intelligence agencies to get a secretive court's permission before accessing the records. It is not clear how the changes Obama announced might affect the legal fight.
Follow Sam Hananel on Twitter at http://twitter.com/SamHananelAP