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The effort has been under way at least since last summer, Hersh said on CNN's "Late Edition."
In an interview on the same program, White House Communications Director Dan Bartlett said the story was "riddled with inaccuracies."
"I don't believe that some of the conclusions he's drawing are based on fact," Bartlett said.
Iran has refused to dismantle its nuclear program, which it insists is legal and is intended solely for civilian purposes. (Full story)
Hersh said U.S. officials were involved in "extensive planning" for a possible attack -- "much more than we know."
"The goal is to identify and isolate three dozen, and perhaps more, such targets that could be destroyed by precision strikes and short-term commando raids," he wrote in "The New Yorker" magazine, which published his article in editions that will be on newsstands Monday.
Hersh is a veteran journalist who was the first to write about many details of the abuses of prisoners Abu Ghraib in Baghdad.
He said his information on Iran came from "inside" sources who divulged it in the hope that publicity would force the administration to reconsider.
"I think that's one of the reasons some of the people on the inside talk to me," he said.
Hersh said the government did not answer his request for a response before the story's publication, and that his sources include people in government whose information has been reliable in the past.
Hersh said Bush, Vice President Dick Cheney and Defense Secretary Donald Rumsfeld view Bush's re-election as "a mandate to continue the war on terrorism," despite problems with the U.S.-led war in Iraq.
Last week, the effort to find weapons of mass destruction in Iraq -- the Bush administration's stated primary rationale for the war -- was halted after having come up empty.
The secret missions in Iran, Hersh said, have been authorized in order to prevent similar embarrassment in the event of military action there. (Full story)
"The planning for Iran is going ahead even though Iraq is a mess," Hersh said. "I think they really think there's a chance to do something in Iran, perhaps by summer, to get the intelligence on the sites."
He added, "The guys on the inside really want to do this."
Hersh identified those inside people as the "neoconservative" civilian leadership in the Pentagon. That includes Rumsfeld, Deputy Defense Secretary Paul Wolfowitz and Undersecretary of Defense Doug Feith -- "the sort of war hawks that we talk about in connection with the war in Iraq."
And he said the preparation goes beyond contingency planning and includes detailed plans for air attacks:
"The next step is Iran. It's definitely there. They're definitely planning ... But they need the intelligence first."
The Bush administration has been carrying out secret reconnaissance missions to learn about nuclear, chemical and missile sites in Iran in preparation for possible airstrikes there
The effort has been under way at least since last summer