Bryan Whitman, a Pentagon spokesman, said on Friday: "That was rumoured a year ago and never proved to be confirmed."
Earlier, Hussain Kamal, Iraq's deputy interior minister, said in a television interview that al-Zarqawi had been arrested by security forces in Falluja, but released because the forces did not know who he was.
However, speaking later to Reuters news agency, Kamal said the story was many months old and contained no new information.
"More than a year ago the Iraqi police in Falluja captured Zarqawi but released him after three or four hours because they did not recognise him," he told Reuters.
"We captured a Saudi terrorist ... and he told us this information," he said. "I said that before."
"Things weren't stable in Falluja and the Interior Ministry was trying to organise; that's why they didn't recognise him," Kamal said, adding: "It won't be long before we capture him again though."
"It won't be long before we capture him again"
Iraqi deputy interior minister
His comments raised questions over the effectiveness and capability of Iraq's security forces a day after the apparent success of national elections held to form a new parliament.
Al-Zarqawi, the alleged frontman of al-Qaida in Iraq and mastermind of numerous bombings, armed attacks, hostage murders and other acts of violence, has a $25 million US bounty on his head.
US military forces in Iraq have claimed to have killed or captured a number of al-Zarqawi's top operatives and said they have come close to capturing al-Zarqawi himself on a number of occasions.
Major-General Rick Lynch, a spokesman for the US-led multinational force in Iraq, said last month: "We come close to Zarqawi continuously and at one point in time, in the not too distant future, we are going to get Zarqawi."
Al-Zarqawi, who was born in Jordan, has only one leg after being injured fighting for the Taliban in Afghanistan.
He has been sentenced to death in his home country for the 2002 murder of a US diplomat in the capital, Amman.
Unlike Osama bin Laden, al-Zarqawi has never released a videotaped message.
Only grainy identity shots, old images from Afghanistan and more recent photos of a portly, grizzled figure give any clue as to his appearance.