The news followed a spate of violence in the country, including the killing of 49 unarmed Iraqi army recruits by militants loyal to al-Qaida ally Abu Musab al-Zarqawi on Sunday.
Mohamed ElBaradei, head of the International Atomic Energy Agency, will immediately report the matter of the missing explosives to the U.N. Security Council, agency spokeswoman Melissa Fleming said.
ElBaradei learned of the disappearance on Oct. 10 and alerted Washington of the seriousness of the matter on Oct. 15, Fleming said.
U.S. weapons experts fear the explosives could be used in bombing attacks against U.S. or Iraqi forces, which have picked up leading up to the country's elections in January, reported The New York Times, which broke the story Monday.
The explosives were under IAEA control until the U.S.-led invasion in March 2003.
Iraq was permitted to keep some of its explosives for mining purposes after the IAEA completed its dismantling of Saddam's covert nuclear weapons program after the 1991 Gulf war, Reuters reported.
Meanwhile, the bodies of 49 Iraqi National Guard recruits, lined up and executed by insurgents, were found on a roadside north of Baghdad, Iraqi officials said Sunday.
The mass killing occurred just after sunset Sunday near the army's main training base in Kirkush, said Col. Adnan Abdul-Rahman, a spokesman for the interim Iraqi Ministry.
The recruits were riding in three buses to begin a 20-day leave when they were stopped at a checkpoint manned by insurgents dressed as Iraqi police, residents said, according to Abdul-Rahman.
Most of the recruits appeared to have filed off the buses, lined up in four rows and lain down before they were shot, the Post reported. Abdul-Rahman said most of the recruits had their hands tied behind their backs.
Guerillas also killed a U.S. diplomat -- Ed Seitz, an agent with the State Department's Bureau of Diplomatic Security -- in a mortar attack on a U.S. base near Baghdad airport on Sunday. He is believed to be the first American diplomat killed in Iraq since last year's U.S.-led invasion.
And insurgents firing mortars at an Iraqi National Guard checkpoint north of Baghdad on Monday killed a civilian driver and wounded his wife, police said, according to Reuters.
Meanwhile, hundreds of demonstrators gathered outside the CARE International office in Baghdad, demanding the release of Margaret Hassan, who directs the office. She was kidnapped by a group of armed men as she was driving to work Oct. 19.
Hassan, a British-Iraqi, had spent years in the country helping the disabled.
"Freedom for Margaret," said one banner, according to Reuters. "Please release Margaret Hassan who has helped us," read another.
Al-Jazeera television aired a video Friday of a tearful Hassan appealing to the British government to save her.