The official was briefed on the investigation but was not authorized to discuss the matter by name and spoke on condition of anonymity.
The official says the breach is believed to have targeted some individual reporters, but the newspaper's network was not compromised.
CNN first reported the violation.
The news comes as federal authorities investigate a breach of the Democratic National Committee that outside cybersecurity experts have attributed to Russian intelligence agencies.
New York Times spokeswoman Eileen Murphy did not immediately respond to a request seeking comment.
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