Colonel David Perkins, at the time the commander of the 2nd Brigade of the 3rd Infantry Division, said the soldiers saw some conventional munitions and a white powdery substance that was tested because of fears of chemical agents.
Besides testing the substance, which proved negative for chemical or biological agents, the soldiers did not do a detailed inventory of what they found during the little more than two days they were at the site from April 3 to April 6, 2003, he said.
"They were doing I would say probably cursory, obvious kinds of things," Perkins said in an interview with reporters, referring to troops from the brigade's 3-15 Infantry Battalion which was sent into to clear out Iraqi forces defending the weapons facility.
In searching warehouses and bunkers they were primarily concerned with weapons of mass destruction, and particularly chemical weapons.
The brigade's top priority, moreover, was to push north and engage the Medina Division of Iraq's Republican Guard defending Baghdad, he said.
"The main focus was not go back and do a very precise inventory of how many shells and things like that because it was just not the threat at the time," he said.
Perkins said he did not recall whether his forces were aware that the site contained materials that had been put under seal by the International Atomic Energy Agency.
Some 380 tons of high explosives that could be used in a trigger for a nuclear device as well as in conventional weapons were last seen at the site by IAEA monitors in March.
Earlier this month, the Iraqi government reported to the IAEA that the explosives were missing, apparently looted from the Al Qaqaa after the war.
The disappearance has become a major issue in the US presidential campaign, with Democratic candidate John Kerry arguing that it showed the administration's failure to secure Iraq, prompting President George W. Bush to lash out at Kerry for making "wild charges."
Pentagon officials have said they do not know what happened to the material, but suggest the Iraqis may have moved it from Al Qaqaa before US troops arrived.
The 3-15 Infantry battalion, the first known US unit of significant size to enter Al-Qaqaa, was followed by the 2nd Brigade of the 101st Airborne Division on April 10, the Pentagon said. It stayed on the perimeter of the complex, however, it said.
"Exploitation teams" from Task Force 75, a unit formed to hunt for weapons of mass destruction, visited the site on May 8, May 11 and May 27, officials said.
Pentagon spokesman Larry DiRita said they found ordnance at the site, but nothing under IAEA seal. It was unclear how much or what type of ordnance was found, or what was done with it.
Perkins had a list of some 300 sensitive weapons sites when his troops left Kuwait, but once inside Iraq they found ammunition and weapons had been dispersed in stockpiles all over the countryside, and that sites were sometimes empty or half full.
The Al Qaqaa site -- a large walled compound many acres in size and containing about 80 buildings and 30 to 40 bunkers -- was "like a dozens of others we had run into prior to it," he said.
Located on the east side of the Euphrates, it was being used as a fortified position by 100 to 200 Iraqi soldiers who fired from it at 3rd Infantry Division vehicles as they crossed a bridge over the river on their way to Baghdad.
A mechanized company and mortar platoon from the 3-15 Infantry Battalion was sent to take the compound in order to secure the bridge, Perkins said.
"This site when we came to it was open, forces were moving in and out of it," he said.
"Some of the warehouse doors were open. The guys would drive by. If they were fighting they would look in and see what was there. So it was not hermetically sealed," he said.
Perkins said he believe it would have "almost impossible" to loot facility of hundreds of tons of high explosives between the time his forces were there and May when the US exploitation teams arrived.
The roads, he said, were "kind of a redball express, I mean just continual US vehicles pushing toward Baghdad."
"So it would really be very highly improbable that somehow, somebody, the enemy, put this together this convoy of trucks, anbd sneaks them in and loads them up in the dark of night, and infiltrates in you convoy and moves out," he said.