Secret missions have been going on at least since last summer with the goal of identifying target information for up to 26 suspected sites, the magazine said in its edition published Monday.
A US commando task force in South Asia has been penetrating into eastern Iran in a hunt for underground nuclear-weapons installations, a former high-level intelligence official told the magazine.
"This is a war against terrorism, and Iraq, is just one campaign," the official told the magazine. "The Bush administration is looking at this as a huge war zone. Next, we're going to have the Iranian campaign."
Defense Secretary Donald Rumsfeld and his deputy Paul Wolfowitz "want to go into Iran and destroy as much of the military infrastructure and possible," a top government consultant with close ties with the Pentagon told the magazine.
White House counselor Dan Bartlett said on CNN's "Late Edition" that the New Yorker report was "riddled with inaccuracies," and that the Bush administration would continue to work through diplomatic initiatives.