The question of whether Vice President Dick Cheney followed proper procedures in ordering the shoot-down of U.S. airliners on September 11 is one of many new issues raised in the remarkably detailed, chilling account laid out in dramatic presentations last week by the 9-11 commission. Newsweek has learned that some on the commission staff were, in fact, highly skeptical of the vice president's account and made their views clearer in an earlier draft of their staff report, Washington Bureau Chief Daniel Klaidman and Senior Editor Michael Hirsh report in the June 28 issue of Newsweek (on newsstands Monday, June 21).

The commission's detailed report notes that after two planes had crashed into the World Trade Center and combat patrols were in the air, a military aide asked for shoot-down authority, telling Cheney that a fourth plane was "80 miles out" from Washington. Cheney didn't flinch, the report said. "In about the time it takes a batter to decide to swing," he gave the order to shoot it down, telling others the president had "signed off on that concept" during a brief phone chat. When the plane was 60 miles out, Cheney was again informed and again he ordered: take it out.

But according to one knowledgeable source, some staffers "flat out didn't believe the call ever took place." Both Cheney and the president testified to the commission that the phone call took place. When the early draft conveying that skepticism was circulated to the administration, it provoked an angry reaction. In a letter from White House lawyers last Tuesday and a series of phone calls, the White House vigorously lobbied the commission to change the language in its report. "We didn't think it was written in a way that clearly reflected the accounting the president and vice president had given to the commission," White House spokesman Dan Bartlett tells Newsweek. Ultimately the chairman and vice chair of the commission, former New Jersey governor Thomas Kean and former Rep. Lee Hamilton -- both of whom have sought mightily to appear nonpartisan -- agreed to remove some of the offending language. The report "was watered down," groused one staffer.

The 9-11 commissioners found themselves engaged in another testy dispute, especially with Cheney, over the ties between Saddam Hussein and Osama bin Laden. The vice president insisted in short-tempered public remarks last week that the commission had agreed the Iraq-Qaeda links were extensive. But commission vice chair Lee Hamilton acknowledged to Newsweek the commissioners had serious differences with the administration. "We didn't have any evidence of collaboration or cooperation," Hamilton said flatly. He added that bin Laden's ties "to Iran and Pakistan were certainly stronger than any tie he had to Iraq."

The vice president also reasserted his belief that a long-alleged meeting between 9/11 hijacker Muhammad Atta and an Iraqi intel agent on April 9, 2001, in Prague might have occurred. Some 9-11 staffers said they were astonished by this: their report, citing cell-phone records, concludes unambiguously that Atta could not have been in Prague on that date; he was in Florida. Newsweek has also learned that Czech investigators and U.S. intelligence have now obtained corroborated evidence which they believe shows that the Iraqi spy who allegedly met Atta was away from Prague on that day.