The website, NSA.gov, went down in the afternoon, setting off speculation on Twitter that the site may have suffered a denial of service attack by hackers.
But an NSA spokesperson denied the claims, saying they were "not true."
"NSA.gov was not accessible for several hours tonight because of an internal error that occurred during a scheduled update. The issue will be resolved this evening," the spokesperson added.
"Claims that the outage was caused by a distributed denial of service attack are not true."
The website was operational again around 10:30 pm (0230 GMT Saturday).
The hacker group Anonymous joked about the incident in a tweet, without saying if it had played any role. "Aw don't panic about nsa.gov being down. They have a backup copy of the Internet," it said.
The loosely organized, international hacker collective has frequently clashed with US authorities over file-sharing as well as allowing banks to handle donations to the anti-secrecy group WikiLeaks.
The NSA has been at the center of a furor over its vast electronic surveillance operations, revealed in a series of leaks from former intelligence contractor Edward Snowden, who has obtained asylum in Russia.
For the latest tech news and reviews, follow Gadgets 360 on X, Facebook, WhatsApp, Threads and Google News. For the latest videos on gadgets and tech, subscribe to our YouTube channel. If you want to know everything about top influencers, follow our in-house Who'sThat360 on Instagram and YouTube.