"Done wrong," he said, "it will sort of hoard everything into Washington, and somebody will have to decide at a high level who gets to look at it. And that would be a mistake."
Brown made clear that his reservations extended to the commission's recommendation that the CIA no longer direct covert paramilitary operations and that, instead, the Special Operations Command assume responsibility for such activities.
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The commission concluded that the Special Operations Command is best qualified to direct such operations and that military professionals should be running operations in which weapons greater than side arms are needed.
But Brown called the issue of CIA involvement very complex and said the agency might still have a role in paramilitary actions.
"I just think we need more study on it," he said.
The Pentagon's appeal for careful consideration left some committee members suspecting an attempt to undercut the recommendations.
"I'd like to ask in plain English, because I've listened now for several hours today, whether the Pentagon is going to put its weight behind the recommendations of the 9/11 commission," said Rep. Jim Cooper (D-Tenn.). "Because I am very worried we're hearing a lot of sweet talkin', slow walkin' here."
Wolfowitz denied that the Pentagon is playing an obstructionist role. He said that the commission "correctly identified important areas where we can do a lot better," and he offered assurances that Pentagon lawyers are working with others in the administration on the recommendations.
Staff writer Helen Dewar contributed to this report.