The lawsuit was filed by the Electronic Frontier Foundation, which represents the unusually broad coalition of plaintiffs, and seeks an injunction against the NSA, Justice Department, FBI and directors of the agencies.
Filed in federal court in San Francisco, it challenges what the plaintiffs describe as an "illegal and unconstitutional program of dragnet electronic surveillance."
The suit came after former NSA contractor Edward Snowden leaked details about NSA surveillance programs earlier this year, revealing a broad U.S. intelligence program to monitor Internet and telephone activity to ferret out terror plots.
Snowden, who has been charged with spying and theft of government property, has spent the past three weeks in the Moscow airport transit zone.
On Tuesday, he submitted a request for temporary asylum in Russia, his lawyer said, claiming he faces persecution from the U.S. government and could face torture or death.
NSA public affairs deferred comment on the Electronic Frontier Foundation lawsuit to the Justice Department. A Justice Department spokesman did not immediately respond to a request for comment.
In the suit, the coalition demands that the federal government return and destroy any telephone communications information in its possession. It also wants a jury trial on the allegations contained in the suit.
The plaintiffs include the First Unitarian Church of Los Angeles, the Council on American Islamic Relations Foundation, Greenpeace, Human Rights Watch, Students for Sensible Drug Policy and others.
The federal government has "indiscriminately obtained, and stored the telephone communications information of millions of ordinary Americans as part of the Associational Tracking Program," the lawsuit states.
Last month, the American Civil Liberties Union filed a similar lawsuit in federal court in New York asking the government to stop the phone tracking program. Several other civil libertarian organizations have also filed legal actions.
A legal expert said the biggest challenge that plaintiffs will face is proving they have actually been wiretapped or been a victim of surveillance.
"But it's now clear that virtually everyone's phone call records can be gathered in this metadata collection program, so I believe they do have standing," said University of Chicago law professor Geoffrey Stone.
Other legal issues include whether the surveillance constitutes a violation of the Fourth Amendment, which guards against unreasonable searches and seizures.
In addition, George Washington University law professor Jonathan Turley said the Obama administration will likely argue, as it has in the past, that the surveillance is protecting national security.
"It's distressing that until the Snowden disclosures, the administration insisted that any discussion of these surveillance programs would cause grave national security problems," Turley said. "What's fascinating is that after Snowden came forward, the administration didn't hesitate a second in discussing the surveillance in public realm."