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WASHINGTON — As the war in Iraq deteriorated, a senior American intelligence analyst went public in 2005 and criticized President George W. Bush’s administration for pushing “amateurish and unrealistic” plans for the invasion two years before.

Now that same man, Gregory Hooker, is at the center of an insurrection of United States Central Command intelligence analysts over America’s latest war in Iraq, and whether Congress, policy makers and the public are being given too rosy a picture of the situation.

As the senior Iraq analyst at Central Command, the military headquarters in Tampa that oversees American military operations across the Middle East and Central Asia, Mr. Hooker is the leader of a group of analysts that is accusing senior commanders of changing intelligence reports to paint an overly optimistic portrait of the American bombing campaign against the Islamic State. The Pentagon’s inspector general is investigating.

Although the investigation became public weeks ago, the source of the allegations and Mr. Hooker’s role have not been previously known. Interviews with more than a dozen current and former intelligence officials place the dispute directly at the heart of Central Command, with Mr. Hooker and his team in a fight over what Americans should believe about the war.

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Gregory Hooker is critical of reports on the ISIS fight.
Mr. Hooker, who declined to comment, has been an Iraq analyst for more than two decades. Some on his team were at Central Command, or Centcom, when American troops poured into Iraq in 2003. The analysts remained focused on the country long after President Obama officially ended the war in 2011.

“This core group of Iraq analysts have been doing this for a long time,” said Stephen Robb, a retired Marine colonel and a former head of the Centcom Joint Intelligence Center. “If they say there’s smoke, start looking for a firehouse.”

The investigation has repercussions beyond the question of whether the American-led bombing campaign in Iraq and Syria is succeeding. The allegations call into question how much the president — this one or the next — can rely on Centcom for honest assessments of military operations in Iraq, Afghanistan, Yemen and other crisis spots.

In some ways, the Iraq team’s criticism mirrors the disputes of a decade ago, when Mr. Hooker wrote a research paper saying the Bush administration, over many analysts’ objections, advocated a small force in Iraq and spent little time thinking about what would follow the invasion.

That dispute was separate from the battle over flawed intelligence assessments by the C.I.A. and other spy agencies that Saddam Hussein had weapons of mass destruction. Central Command did not contribute significantly to those assessments.

Several current and former officials said that it was the two most senior intelligence officers at Centcom — Maj. Gen. Steven Grove and his civilian deputy, Gregory Ryckman — who drew analysts’ ire with changes in draft intelligence assessments. But why the assessments were changed remains an open question. Some analysts suggested that leaders in Tampa feared that reporting bad news might anger the White House. Others described an institutional bias that makes it hard for the military to criticize its own operations.

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Centcom’s leader, Gen. Lloyd J. Austin III, was chosen for the job in part because the White House regarded him as a steady, cautious loyalist who would execute military operations in the Middle East with little drama — an especially important consideration after the contentious relationship between the White House and Gen. James Mattis, the previous Centcom commander. General Austin gave testimony last week to the Senate Armed Services Committee that was roundly criticized by some lawmakers as being an overly positive assessment of the war’s progress.

Centcom’s mammoth intelligence operation, with some 1,500 civilian, military and contract analysts, is housed at MacDill Air Force Base in Tampa, in a bay front building that has the look of a sterile government facility posing as a Spanish hacienda. In banks of plain cubicles, the analysts try each day to measure the progress of war.

That effort has long been difficult, particularly in campaigns without traditional armies and clear battle lines. During the war in Vietnam, generals were criticized for measuring success in body counts. In the fight against the Islamic State, also known as ISIS or ISIL, the military issues daily reports that suggest tactical victories but offer little hint about how the war is going.

“One airstrike struck an ISIL tactical unit and destroyed an ISIL cache, three ISIL fighting positions and one ISIL motorcycle,” a report this month said. “Near Ramadi, one airstrike destroyed an ISIL vehicle.”

Brian Hale, a spokesman for the director of national intelligence, played down the significance of Centcom’s conclusions in shaping the thinking of senior policy makers, including Mr. Obama, about the war. In a statement on Wednesday he said that Centcom and other military commanders do not provide “broad or strategic assessments.”

The success of daily airstrikes, experts say, can give the illusion of progress, particularly for Centcom commanders who are judged in Washington on their ability to carry out a successful mission. Iraq analysts, officials said, are less optimistic.

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“You can get pulled into watching the laser dot on a target and watching it blow up,” said Kevin Benson, a retired Army colonel who teaches intelligence analysis to officers at Fort Leavenworth, Kan. “After that, it can be hard to hear that you’re not making progress, because you saw it.”

Analysts like Mr. Hooker and his team are supposed to be immune from such pressure because they are employed by the Defense Intelligence Agency. In practice, though, the analysts are reviewed by officials at Centcom.

Although critics have suggested that the bombing campaign’s stalemate proves the need for more troops in Iraq, colleagues say Mr. Hooker’s team is not advocating that approach. “I don’t know anyone outside of a political commercial who thinks we need to send large numbers of troops into Iraq,” said one intelligence official who has worked closely with the Centcom analysts.

Instead, analysts say the dispute centers on whether the military is being honest about the political and religious situation in Iraq and whether a bombing campaign can change it.

“What are the strategic objectives here? There are none. This is just perpetual war,” said David Faulkner, the former targeting director at Centcom who worked alongside the Iraq analysts. “People say: ‘Oh, you’re military. You like that.’ No, we don’t.”

Current and ex-officials said tension about how to portray the war’s progress began almost at the start of the campaign last summer, when Mr. Obama authorized strikes against Islamic State fighters in Iraq and later expanded the bombings to Syria.

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Early this year, one former official said, Mr. Hooker’s team concluded that, despite public statements to the contrary, airstrikes against Islamic State-held refineries had not significantly weakened its finances because it had built makeshift refineries to sell oil on the black market. But the finding was not distributed outside Centcom, the ex-official said.

Over this past year, analysts felt pressure to keep their assessments positive. In order to report bad news, current and former officials said, the analysts were required to cite multiple sources. Reporting positive news required fewer hurdles. Senior officials sent emails cautioning against using pessimistic phrases that they said were more likely to get attention, according to one former official. In some instances, officials said, conclusions were completely changed.

Anger among analysts grew so intense that in the spring, Mr. Hooker’s civilian boss, William Rizzio, confronted his superiors about the problems. Mr. Rizzio, a retired Marine colonel who had gradually come to take the side of the analysts in the dispute, had meetings with General Grove and Mr. Ryckman. It is unclear what transpired in the meetings, but three people with knowledge of the situation, who, like some others interviewed, spoke on the condition of anonymity because the matter is part of the inspector general’s investigation, said the result was that Mr. Rizzio was punished for siding with the analysts. He was temporarily reassigned, and analysts were left wondering what happened to him after his name was scraped off the front of his office at Centcom’s Joint Intelligence Center.

Mr. Rizzio, who has since returned to his position, declined to be interviewed.

His concerns gained a more sympathetic hearing several months later, when officials began speaking to the Pentagon’s inspector general, who opened his investigation in July. Officials would not say if Mr. Hooker was the first analyst to do so.

The inspector general’s investigation turned a quiet matter into one of the most high-profile intelligence disputes since officials issued new rules that encourage dissenting views. Those rules were intended to prevent a repeat of the debacle over weapons of mass destruction in Iraq.

The investigation has put this team of analysts, who for years worked in relative obscurity, at the center of a dispute that has the attention of intelligence officials across the government.

“Signing onto a whistle-blowing complaint can easily be a career-ender,” David Shedd, a former acting head of the Defense Intelligence Agency, wrote in a column this week on Defense One, a national security news website. “The nation’s analytic professionals are watching closely to see how it is handled.”

Correction: September 24, 2015
An earlier version of this article misstated the year that President Obama officially ended the Iraq war. It was 2011, not 2009.
Kitty Bennett contributed research.

By MARK MAZZETTI and MATT APUZZOSEPT. 23, 2015

A version of this article appears in print on September 24, 2015, on page A1 of the New York edition with the headline: Military Analyst Again Raises Red Flags on Progress in Iraq. Order Reprints| Today’s Paper|Subscribe

Find this story at 23 September 2015

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