Computer users who logged on in Beijing, Shanghai and Guangzhou received a message that the site was not available when they tried to connect on Friday morning, the paper said. Some users were cut off as early as Thursday evening, it said.
The Web site remained inaccessible from Beijing Saturday.
It was not clear whether the move was meant to block specific content on the newspaper's Web site or whether it was a return to stricter censorship of the Internet in general. Beijing loosened some media and Internet controls during the 2008 Summer Olympics - gestures that were meant to show the international community that the games had brought greater freedom to the Chinese people.
A spokesman for the Foreign Ministry said it does not deal with Web sites. The Ministry of Industry and Information Technology, which regulates the Internet, could not be reached for comment.
Earlier this week, Foreign Ministry spokesman Liu Jianchao defended China's right to censor Web sites that have material deemed illegal by the government, saying that other countries regulate Internet usage, too.
During the August games, China allowed access to long-barred Web sites such as those of the British Broadcasting Corp. and Human Rights Watch after an outcry from foreign reporters who complained that Beijing was failing to live up to its pledges of greater media freedom.
The New York Times said Beijing had blocked the Chinese-language Web site of the BBC, and Web sites of Voice of America, Asiaweek, and Ming Pao, a Hong Kong newspaper, earlier in the week. But apart from Ming Pao, the sites were all accessible Friday, it said.
Ming Pao's online site was still inaccessible Saturday in Beijing.
China has the most online users in the world with more than 250 million, but it has also put in place a sophisticated system to police Web sites for sensitive material and routinely blocks sites that support Tibetan independence or the region's spiritual leader, the Dalai Lama.
A spokeswoman for The Times, Catherine J. Mathis, told the paper that there did not appear to be a technical issue. Users in Japan, Hong Kong, and the U.S. were also not experiencing difficulties, the paper said.