The Qaqaa facility once played a key role in Saddam Hussein's efforts to build a nuclear bomb, the IAEA said.
Before the war, IAEA inspectors had kept tabs on the so-called "dual use" explosives because they could have been used to detonate a nuclear weapon.
The loss is of particular concern because the two substances - known as HMX and RDX - are easily transportable. They are non-volatile and require a detonation cap to release their energy.
They pose "a high explosives risk" to coalition troops in Iraq, the Times quoted a Bush administration figure as saying.
The Qaqaa facility was under the control of the US-led Coalition Provisional Authority until it handed sovereignty to the interim government on June 28.
"After the collapse of the regime, our liberation, everything was under the coalition forces, under their control," Iraqi Science and Technology Minister Rashad Omar told the newspaper.
"So probably they can answer this question, what happened to the materials."