In a ceremony at the White House, Bush presented the medals to retired general Tommy Franks, former CIA director George Tenet and former Iraq administrator L. Paul Bremer.
"This honor goes to three men who have played pivotal roles in great events and whose efforts have made our country more secure and advanced the cause of human liberty," Bush said.
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Franks, a retired four-star Army general, who had commanded US forces in Afghanistan and Iraq, got the award despite being criticized for not asking for more US troops to check the chaos after Baghdad fell.
Tenet, who resigned in July after seven years as CIA chief, has been criticized for intelligence failures before the September 11, 2001 attacks and the intelligence before the Iraq war alleging the existence of weapons of mass destruction in Iraq.
No such weapons have been found.
Bremer oversaw the transfer of power to an interim Iraqi government in June.
But he raked up a controversy after leaving Iraq by saying the US had never sent enough troops to Iraq, and has been criticized for disbanding the former Iraqi army and abolishing Iraq's defense ministry, putting a heavy burden on US troops to train Iraq forces.