On its official Twitter account, the New York Times said it was "experiencing a server issue that has resulted in our e-mail and Web site being unavailable."
The outage started around 11:30 a.m. EDT and lasted until about 1 p.m. Both the newspaper site, NYTimes.com, and its corporate site, NYTco.com, were down.
The newspaper called the outage an "internal issue," with Times officials saying late Wednesday it was the result of "a failure during regular maintenance of NYTimes.com and not the result of a cyberattack."
Not everyone was convinced of that, though.
"My suspicion leads me to believe that this is not really an internal issue," Cedric Leighton, a former National Security Agency official, told FoxBusiness.com. "This is something that goes way beyond that."
Other experts were less sure.
"There's a strong likelihood that someone internally [messed] up and also probably as good of a chance that it could have been external," said Dov Yoran, head of malware analysis and threat intelligence firm Threat Grid.
2014: NFL Cheerleaders [PHOTOS]
Apple releases fix for 'Shellshock' virus