WASHINGTON – The Pentagon, in an extraordinarily blunt statement, disputed the accuracy and questioned the motives of a report in this week’s New Yorker alleging American assets have covertly infiltrated Iran to identify possible nuclear targets for air strikes.

The piece by veteran reporter Seymour Hersh, in the issue that hit newsstands yesterday, says the president signed executive orders allowing the Pentagon to run covert operations against terrorist targets in 10 separate countries, effectively cutting Congress and the CIA out of the decision loop. One such operation involves teams of operatives dispatched into Iran to identify potential targets in the country’s nuclear, chemical weapons and missile programs, it says.

A long statement from Pentagon spokesman Lawrence DiRita said Mr. Hersh’s sources “feed him with rumor, innuendo, and assertions about meetings that never happened, programs that do not exist, and statements by officials that were never made.” At no point, however, did the Pentagon statement specifically dispute that there were teams sent inside Iran to identify potential targets.

The latest flap over Mr. Hersh’s reporting highlights high-stakes intergovernment negotiations over Iran policy. A number of former officials from previous administrations have already endorsed a diplomatic approach, whereby America would join Britain, France, and Germany in persuading Tehran to dismantle a program the Iranians have said is solely for the production of energy.

Hawks outside the administration have called for a selective bombing campaign to set back the Iranian nuclear program, which American and Israeli intelligence estimate could produce nuclear fuel within three years.

In particular, Mr. DiRita took aim at a section of the story in which Mr. Hersh writes that civilian Defense Department officials “have been working with Israeli planners and consultants to develop and refine potential nuclear, chemical-weapons, and missile targets inside Iran.” Mr. DiRita accused Mr. Hersh, who is Jewish, of “building on links created by the soft bigotry of some conspiracy theorists.”

Mr. Hersh dismissed that accusation. “The suggestion that this is coming from some anti-Israeli cabal is ridiculous,” he told The New York Sun yesterday.

The editor of the New Yorker, David Remnick, wrote in an e-mail: “I remember well that Mr. DiRita said not long ago that Mr. Hersh’s stories about Abu Ghraib were nothing more than (please forgive me, it’s his language) nothing more than ‘a lot of crap’ thrown against a wall, etc. In these new remarks, the spokesman outdoes himself. The pattern of invective and innuendo – coupled with a failure to address the article directly – is, unfortunately, growing familiar.”

Mr. Hersh has ruffled the feathers of the Pentagon before. He broke most of the stories about how American GIs and individuals attached to the CIA abused Iraqis at Abu Ghraib prison.

Last May, Mr. DiRita called Mr. Hersh’s reporting, which in some cases has been borne out in documents released through the Freedom of Information Act, “outlandish, conspiratorial, and filled with error and anonymous conjecture.”

In those stories, Mr. Hersh wrote that policy decisions made in Washington at the highest levels condoned the sexual torture disclosed in photographs this summer from Abu Ghraib.

Earlier this month, a memo defining the limits of acceptable interrogation methods written by then-White House counsel Alberto Gonzales was the topic of intense questioning from senators at the hearing for Mr. Gonzales’s nomination for attorney general.

Mr. Hersh has also written that Iraqi Prime Minister Allawi carried out political assassinations in the 1970s for Saddam Hussein. This account was disputed in comments to the Sun by both CIA officials who worked with Mr. Allawi after the Gulf War and his colleagues in exile.

Since 1998, senior officials from the Bush and Clinton administrations have had regular meetings with their Israeli counterparts on Iran’s nuclear program, arranged through the State Department. In these meetings, even signals intelligence, often the most closely held information by spy services, has been shared regarding the nuclear aspirations and program of the Islamic republic, according to former American and Israeli officials who have been briefed on the meetings.

The Pentagon has also started planning a massive microwave military communication network linking bases in countries that surround Iran, as the Sun reported Friday. The network would eventually connect bases in Qatar, the United Arab Emirates, and Iraq to American facilities in Afghanistan.

In his story, Mr. Hersh says Deputy Secretary of Defense Wolfowitz and Undersecretary of Defense Feith have privately advocated for an invasion of Iran. The Sun has reported in the past that Messrs. Feith and Wolfowitz have favored increased financial assistance to the nonviolent elements of the Iranian democracy movement. Mr. DiRita yesterday said the views ascribed to the two officials in Mr. Hersh’s article were wrong.

A former analyst on Iran and Iraq who worked for Mr. Feith, Michael Rubin, yesterday said, “The evidence which Sy Hersh brings to light makes it clear the purge in the CIA has not gone far enough. There are two possibilities. If the story is untrue, then senior CIA officials are lying in order to hurt the president and affect U.S. policy. If they are telling the truth, their hatred of the president and desire to shape policy makes them willing to put lives at risk.”

Mr. Hersh said he vetted his story very carefully to make sure he would not endanger the lives of individuals conducting the secret operations.