The US is playing down the significance of a UN letter saying almost 350 metric tons of high explosives went missing from an Iraqi base after the war.
The IAEA said the US-led coalition had been warned about the danger
White House spokesman Scott McClellan said there was no risk of nuclear proliferation because of the theft.
It has become a big election issue after President George Bush was accused of incompetence by his Democrat rival.
Meanwhile, some US media reports have queried if the theft happened before US troops arrived at the base at al-Qaqaa.
NBC television reported that one of its correspondents was embedded with the 101st Airborne Division which temporarily took control of the base on 10 April 2003 but did not find any of the explosives.
However, other US outlets, including NBC's own news website, quoted Pentagon officials who said a search of the site after the US-led invasion had revealed the explosives to be intact.
Arms experts say the missing explosives - monitored by the UN nuclear watchdog until the March 2003 invasion - could potentially be used to make a detonator for a nuclear bomb or other explosive device.
US presidential challenger John Kerry condemned the incident as a prime example of what he said was President George W Bush's mishandling of the war in Iraq.
195 metric tons of HMX
141 metric tons of RDX
5.8 metric tons of PETN
"This is... one of the greatest blunders of this administration - and the incredible incompetence of this president and this administration has put our troops at risk and this country at greater risk," Mr Kerry said.
Administration officials, quoted anonymously by US media, criticised the UN watchdog - the International Atomic Energy Agency - for leaking the news at such a sensitive time, a week before the US election.
The Vienna-based IAEA said it had been informed on 10 October by the Iraq interim government that the explosives were missing.
Mr McClellan pointed journalists to the 243,000 munitions destroyed in Iraq since the invasion, and another 163,000 earmarked for destruction.
"The first priority, from our standpoint, was to make sure that this wasn't a nuclear proliferation risk, which it is not," he said.
"These are conventional high explosives... and the president wants to make sure that we get to the bottom of this."
The IAEA last inspected the munitions at al-Qaqaa in January 2003, at which point the HMX explosives had been sealed and tagged.
The agency has not been allowed back into Iraq since the invasion.
Analysts say the theft raises the possibility that some explosives could have found their way into improvised devices used against US-led forces in Iraq, or could do so in the future.
But US officials say the car and roadside bombings that have claimed thousands of lives in the Iraq insurgency have mostly used artillery shells or dynamite.
The explosives lost at Qaqaa consist mainly of 195 tons of HMX (high melting explosives) and 141 tons of RDX (cyclonite) - both key components in plastic explosives.