The newspaper claimed that hackers had stolen reporters' passwords and hunted for files on the investigation, published last October, which claimed that Mr Wen's family had accumulated at least $2.7 billion in "hidden riches" .
The report, which was posted online on Oct 25, embarrassed the Communist Party leadership, coming ahead of a fraught transition to new leaders and exposing deep-seated favouritism at a time when many Chinese are upset about a wealth gap.
"For the last four months, Chinese hackers have persistently attacked The New York Times, infiltrating its computer systems and getting passwords for its reporters and other employees," the newspaper said on Thursday.
"Security experts hired by The Times to detect and block the computer attacks gathered digital evidence that Chinese hackers, using methods that some consultants have associated with the Chinese
The hackers broke into the email accounts of Shanghai bureau chief, David Barboza, who wrote the story on Mr Wen's family, and Jim Yardley, the paper's South Asia bureau chief in India who was previously the Beijing bureau chief, it added.
"Computer security experts found no evidence that sensitive emails or files from the reporting of our articles about the Wen family were accessed, downloaded or copied," said Jill Abramson, the paper's executive editor.
Security experts found evidence that the hackers stole the corporate passwords for every New York Times employee and used those to gain access to the personal computers of 53 employees, most of them outside The New York Times's newsroom, the paper said.
"Experts found no evidence that the intruders used the passwords to seek information that was not related to the reporting on the Wen family."
Computer security experts at Mandiant, the company hired by the newspaper, said the hackers tried to "cloak" the source of their attacks "by first penetrating computers at United States universities and routing the attacks through them".
"This matches the subterfuge used in many other attacks that Mandiant has tracked to China."
The Chinese government has repeatedly said it opposes hacking and that China too suffers frequently from these kinds of attacks.