WASHINGTON — As the Bush administration began assembling its case for war, analysts across the U.S. intelligence community were disturbed by the report of a secretive Pentagon team that concluded Iraq had significant ties to Al Qaeda.

Analysts from the CIA and other agencies "disagreed with more than 50%" of 26 findings the Pentagon team laid out in a controversial paper, according to testimony Friday from Thomas F. Gimble, acting inspector general of the Pentagon.

The dueling groups sat down at CIA headquarters in late August 2002 to try to work out their differences. But while the CIA agreed to minor modifications in some of its own reports, Gimble said, the Pentagon unit was utterly unbowed.

"They didn't make the changes that were talked about in that August 20th meeting," Gimble said, and instead went on to present their deeply flawed findings to senior officials at the White House.

The work of that special Pentagon unit — which was run by former Undersecretary of Defense Douglas J. Feith — is one of the lingering symbols of the intelligence failures leading up to the war in Iraq.

The Bush administration's primary justification for invading Iraq was always its assertion that Saddam Hussein possessed weapons of mass destruction. But Iraq's supposed ties to Al Qaeda — and therefore its connection to the Sept. 11 terrorist attacks — were an important secondary argument, and one that resonated with many Americans in the lead-up to the war with Iraq.

The CIA and many other intelligence agencies were wrong in their assessments of Iraq's weapons programs. But the agency was always deeply skeptical about the ties between Iraq and Al Qaeda.

Most of the evidence that Feith's Office of Special Plans cited in making its case for significant collaboration between Baghdad and Al Qaeda has crumbled under postwar scrutiny. The Senate Intelligence Committee has concluded that Saddam Hussein was so wary of the terrorist network that he barred anyone in his government from dealing with Al Qaeda.

Although the Pentagon Inspector General's report released Friday did not address the accuracy of such assessments, it documented the unusual efforts by Defense Department policymakers to bypass regular intelligence channels and influence officials at the highest level of government.

Feith's work was of critical importance to Vice President Dick Cheney, who once referred to the Pentagon team's conclusions as the "best source" for understanding the relationship between Iraq and Al Qaeda.

The activities of Feith's group weren't illegal, Gimble concluded. But they were, "in our opinion, inappropriate, given that the intelligence assessments were [presented as] intelligence products and did not clearly show the variance with the consensus of the intelligence community."

The Pentagon team touted a series of claims that have not survived postwar review. Among them was the allegation that Mohammed Atta, the presumed ringleader of the Sept. 11 hijackers, had met with an Iraqi agent in Prague before the attacks.

A critical question raised by the inspector general's report is whether Feith and his office were just critiquing CIA analysis, or were creating their own intelligence assessment, a role that is supposed to be left to the CIA and other intelligence agencies.

Senate Armed Services Committee Chairman Carl Levin (D-Mich.) noted Friday that Cheney has referred to Feith's work as an "assessment," suggesting it was a formal intelligence document. But Feith maintained in interviews he was not creating an intelligence "product," but was just checking the work of the CIA.

Laurence H. Silberman, a semiretired U.S. appeals court judge and co-chairman of a presidential commission on Iraq's weapons, said it is appropriate to question intelligence.

"Policymakers, whether they are in Defense, State, the White House or Congress, are absolutely entitled to question the intelligence community, look over the material and come up with their own views," he said.

Feith's work had the blessing of his boss, former Defense Secretary Donald H. Rumsfeld. The operation was set up at the behest of then-Deputy Defense Secretary Paul D. Wolfowitz with approval from Rumsfeld, Gimble noted. By most accounts, those three officials had distrust, if not disdain, for the work of the CIA and other intelligence agencies.

But Robert M. Gates, the new secretary of Defense and former CIA director, said that groups outside the CIA and other chartered intelligence agencies should not be involved in freelance analysis.

"Based on my whole career, I believe all intelligence activities need to be carried on by the established institutions, where there is appropriate oversight," he told reporters traveling with him in Europe for meetings on security.

Gimble provided new details on the chain of events leading from the creation of the Feith team, through a series of briefings it made for senior officials and culminating in a presentation before deputies in the National Security Council at the White House.