In the article, a June profile of McChrystal in Rolling Stone magazine, he was reported as making comments seen as disrespectful toward Obama administration officials. But on Monday, Acting Deputy Inspector General Michael S. Child said the inquiry concluded that "not all of the events at issue occurred as reported."
He wrote that "the evidence was insufficient" to judge whether McChrystal or his staff violated Defense Department conduct rules.
The conclusions came too late to change the outcome of the McChrystal affair, widely reported as a case of insubordination by what the article described as a "runaway general." But they could open President Obama and others in the White House to criticism that they acted hastily in accepting McChrystal's resignation.
At the same time, the inspector general's report could be criticized for failing to get to the bottom of what happened. The inquiry relied largely on testimony from active-duty military officers, many of whom apparently testified that they could not recall who had made certain comments quoted in the article.
When the story appeared, McChrystal, one of the Army's most experienced combat commanders, was summoned to Washington for a meeting with Obama. After the meeting, the general announced his resignation and, shortly thereafter, his retirement from the Army. He is now teaching at Yale University and has formed a consulting firm.
The Defense Department's inspector general initiated the review after an earlier report, by the Army's inspector general, faulted some of McChrystal's junior aides. Child said he disagreed with the earlier report's conclusions.
McChrystal declined to comment on the new report. Rolling Stone said in a statement that the review "offers no credible source — or indeed, any named source — contradicting the facts as reported in our story."
The article, by Rolling Stone writer Michael Hastings, recounted several incidents in which unidentified aides to McChrystal made disrespectful and disparaging comments about administration officials, including Vice President Joe Biden, then-national security advisor James L. Jones and Richard C. Holbrooke, who was special envoy to Afghanistan and Pakistan.
In its investigation, the Pentagon inspector general's office said it interviewed 15 witnesses to the incidents, though not McChrystal or Hastings.
"In some instances, we found no witnesses who acknowledged making or hearing the comments as reported. In other instances, we confirmed that the general substance of an incident at issue occurred, but not in the exact context described in the article," the report said.
In perhaps the most damaging incident reported in the article, McChrystal was described talking with his staff about how to answer questions in public about Biden, who had been an internal critic of McChrystal's counterinsurgency strategy and request for 40,000 additional troops.
The article quoted McChrystal as saying, "Are you asking about Vice President Biden? Who's that?" An aide reportedly responded, "Did you say: Bite me?" — apparently a play on Biden's name.
The inspector general's investigation said one witness recalled McChrystal saying, "Who's that?" referring to Biden, and that someone else might have said, "Bite me." But the inquiry concluded: "We were unable to establish the exact words or the speaker."
Rolling Stone said the accounts from unidentified witnesses were "not surprising, given that the civilian and military advisors questioned by the Pentagon knew that their careers were on the line if they admitted to making such comments."
The White House recently moved to soothe relations with McChrystal, naming him to an administration panel overseeing aid to military families. That action was taken April 11; the Pentagon report was completed April 8.