The New York Times said the persistent attacks over the past four months 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.
A statement from the Journal's parent company, Dow Jones & Co, said the newspaper's computer systems had been infiltrated for the purpose of monitoring "the Journal's coverage of China, and are not an attempt to gain commercial advantage or to misappropriate customer information."
Paula Keve, the chief spokeswoman for Dow Jones, said the company had just finished upgrading its network security system.
"We fully intend to continue the aggressive and independent journalism for which we are known," she said.
China's foreign ministry has called The New York Times' accusations "groundless," the BBC said.
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"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 New York Times 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.