The website went down late in the morning and remained down as of 1:30 p.m. EDT.
The newspaper said on Twitter early Wednesday afternoon that it believes the outage stemmed from an internal issue. The outage affected the Times' main news site, along with the company's corporate sites and its email system. The newspaper's mobile phone app also didn't appear to be updating.
Company spokeswoman Eileen Murphy said the problem occurred "within seconds of a scheduled maintenance update" and wasn't believed to be linked to a cyber-attack.
The outage came amid a heavy day of news that included a state of emergency declaration in Egypt as the country continued a crackdown on protesters.
While it was working to restore its website, The Times posted an updated story about the unrest in Egypt on its Facebook page.
Like other newspapers, The Times has focused its growth strategy on digital products in recent years. The newspaper is attempting to offset drops in print subscription revenue by boosting its ranks of digital subscribers. As of June 30, the Times had 738,000 digital subscribers, representing a nearly 40 percent increase from a year ago. Revenue from digital subscriptions in the April-June quarter rose to $38.3 million, up 44 percent from a year ago.
The New York Times Company's stock was down less than 2 percent at $12.05 in afternoon trading.