The paper claimed the attacks coincided with its report into the possibility that the family of Chinese Premier Wen Jiabao had accumulated a multi-billion dollar fortune. It also said the hackers used methods "associated with the Chinese military" to target the emails of the report's writer.
China's foreign ministry has called the accusations "groundless," the BBC said.
"To arbitrarily assert and to conclude without hard evidence that China participated in such hacking attacks is totally irresponsible," said spokesman Hong Lei. "China is also a victim of hacking attacks. Chinese laws clearly forbid hacking attacks, and we hope relevant parties takes a responsible attitude on this issue."
The report infuriated Chinese authorities, who then blocked access to the Times's website in mainland China, reported CNN. The paper said it worked with computer security experts to monitor, study and eject the hackers. By following their movements, it aimed to "erect better defenses to block them" in the future.
The experts accumulated "digital evidence that Chinese hackers, using methods that some consultants have associated with the Chinese military in the past, breached the Times's network."
The New York Times said the hacking initially focused on the computers of David Barboza, the Shanghai bureau chief who wrote the report, and one of his predecessors, Jim Yardley.