Always two sides to a story, especially when the NYTimes is involved. From CNN:
http://www.cnn.com/2004/WORLD/meast/10/26/iraq.explosives/index.html
In a letter to the IAEA dated October 10, Iraq's director of planning, Mohammed Abbas, said the material disappeared sometime after Saddam's regime fell in April 2003, which he attributed to "the theft and looting of the governmental installations due to lack of security."
Baghdad fell on April 9, 2003. According to NBC, troops from the 101st Airborne arrived the next day to find that the material was already gone.
Prior to the Iraq war, the high-grade explosives at Al Qaqaa had been under the control of IAEA inspectors because the material could be used as a component in a nuclear weapon, IAEA spokeswoman Melissa Fleming said. IAEA and other U.N. inspectors left the country in March 2003 before the fighting began on March 19.