A lawsuit filed against the National Security Agency challenging the legality of its telephone metadata tracking programs will proceed, despite the furlough of many federal workers.

So ruled San Francisco-based U.S. District Court Judge Jeffrey S. White, quashing a motion from the Department of Justice (DOJ) to stay the case of "First Unitarian Church of Los Angeles vs. NSA." The defendants' motion cited the "lapse of appropriations" -- meaning the partial shutdown of the federal government -- affecting Department of Justice and NSA employees as the reason for why the case should be put on hold, pending Congress resuming full funding for both agencies.

But Judge White disagreed, issuing a one-page order Tuesday that said simply, "All deadlines shall remain as previously set," Politico first reported.

The lawsuit against the NSA centers on the agency's bulk collection of telephone metadata, and was filed by 22 organizations, including the Electronic Frontier Foundation, which is representing the organizations in court.

[ Has NSA surveillance met its match? See NSA Battles Tor: 9 Facts. ]

In a court filing, the EFF had argued against the government's motion to delay the case, noting that the NSA's surveillance apparatus wasn't furloughed. "Notwithstanding the lack of appropriations, defendants are continuing the bulk collection each day of all the telephone calling records of plaintiffs and hundreds of millions of other Americans," according to a court document filed by the EFF. "Department of Justice lawyers continue to work at that task, including preparing the application for a renewal of the current FISA Court telephone calling records bulk collection order, which expires on or about October 17, 2013." The EFF's filing also referenced a DOJ contingency plan showing that 91% of national security employees were exempted from the furlough.

"If it is essential that the spying continue despite the lack of appropriations, then it is equally essential that the question of whether the spying is lawful also go forward," the EFF argued.

The existence of the NSA metadata collection programs, which sport codenames such as Prism and have been in operation since 2006, were revealed this past summer in documents leaked by former NSA contract employee Edward Snowden. According to the EFF, the lawsuit against the NSA "argues that this spying violates the First Amendment, which protects the freedom to associate and express political views as a group."

Organizations joining the lawsuit include church groups, the California Association of Federal Firearms Licensees, multiple state branches of the Council on American-Islamic Relations, Human Rights Watch and the California chapter of the National Organization for the Reform of Marijuana Laws, as well as other privacy rights groups.