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The global financial institution -- which has been spearheading the response to the eurozone crisis in recent months -- has detailed and market-moving information on the fiscal shape of the world's economies.
"This was a very major breach," an IMF official said, according to the Times, adding that the months-long attack began before former IMF chief Dominique Strauss-Kahn was accused of sexually assaulting a hotel maid in Manhattan.
The IMF could not be reached Saturday, but the Times quoted its spokesman as saying the fund was investigating an incident and was "fully functional."
The Times also reported that the World Bank, which is headquartered across the street from the IMF, had cut the computer link between the two entities out of caution over the incident. The World Bank could not be reached either.
The Times said IMF staff were informed of the attack on Wednesday but the fund did not make any public announcement.
The officials cited by the Times declined to say where the attack might have originated, but the newspaper said it could have been carried out by "spear phishing," where a user is tricked into clicking on a malicious web link or running a program that gives an outsider access to a network.
Earlier this month, the vigilante hackers group "Anonymous" declared an online attack against the IMF over the strict conditions imposed by its bailout for Greece.
Nominations for a new IMF chief to replace Strauss-Kahn -- who resigned last month to battle allegations that he sexually assaulted a Manhattan hotel maid -- closed midnight on Friday.
The closely fought battle between France's Christine Lagarde and Mexico's Agustin Carstens pits Europe -- which has traditionally held the top job -- against fast-rising developing economies demanding a greater global role.