The president added that he did not infer that the two had a "collaborative relationship" on the attacks, a conclusion rejected by the commission investigating the intelligence failures that prevented the United States from warding off the attacks.
"There was a relationship between Iraq and Al Qaeda," Bush insisted to reporters following a meeting with his Cabinet at the White House.
"This administration never said that the 9/11 attacks were orchestrated between Saddam and Al Qaeda," he said.
"We did say there were numerous contacts between Saddam Hussein and Al Qaeda, for example, Iraqi intelligence agents met with [Usama] bin Laden, the head of Al Qaeda in Sudan."
The president added that Saddam gave safe haven to Al Qaeda associate Abu Musab al-Zarqawi (search). An Iraqi interior minister on Thursday alleged that Zarqawi was responsible for a car bombing on Thursday that killed 35 Iraqis as they were signing up to join the nation's new army.
The independent Sept. 11 commission said Wednesday that no evidence exists that Al Qaeda had strong ties to Saddam Hussein.
The report by commission staff, based on interviews with government intelligence and law enforcement officials, said bin Laden asked for help from Iraq in the mid-1990s, but Saddam's government never responded. It claimed "no credible evidence" has emerged that Iraq was involved in the Sept. 11 strikes.
On Capitol Hill, House Minority Leader Nancy Pelosi, D-Calif., suggested that the president "has lost all credibility" because of his claims of a link between Al Qaeda and Iraq.
But John Lehman, a former Navy secretary and Republican member on the commission, dismissed the claims made against Bush.
"There's an attempt by some ... to manufacture a controversy where there is none," Lehman told Fox News.
The Associated Press contributed to this report.