But Mr. Bush, in a speech to defense industry workers in Ohio, expressed confidence that the U.S. will learn the truth about Iraq's weapons programs.
"One thing is for certain: Saddam Hussein no longer threatens America with weapons of mass destruction," he said, to cheers.
Iraq's alleged arsenal of banned biological and chemical weapons and program to develop nuclear weapons were the major rationale for the war against Iraq.
United Nations inspections found no evidence of such weapons, but the Bush administration insisted Saddam's regime was fooling the U.N. teams.
The president said Thursday that Iraqi scientists and officials "are beginning to cooperate, are beginning to let us know what the facts were on the ground."
"And that's important because the regime of Saddam Hussein spent years hiding and disguising his weapons. He tried to fool the United Nations, and did for 12 years, by hiding these weapons," Mr. Bush said. "And so, it's going to take time to find them. But we know he had them. And whether he destroyed them, moved them, or hid them, we're going to find out the truth."
Since the war began, U.S. troops have reported finding chemical protective suits, antidotes to chemical weapons and written plans for chemical warfare, but no actual biological or chemical weapons. Several potential finds have been reported and then discounted. Tests could be ongoing on other recent finds.
U.S. military leaders stress that the focus for American troops is only now turning from fighting Iraqis to finding weapons, and that many sites remain to be checked. Some 1,000 experts are involved in the search.
In an interview with NBC, the president acknowledged that "there's going to be skepticism until people find out there was, in fact, a weapons of mass destruction program." But he added: "We will find them."
This week, six Iraqi scientists and several graduate students say they were told immediately before the war to destroy or hide biological research. They claim the research was for civilian purposes only.
The New York Times reports that an Iraqi scientist has told coalition troops that Iraq began destroying biological and chemical materials in the months before the war, and sent some weapons to Syria.
Initial tests on one of the sites the scientist identified as a dumping ground were positive, the Times reports, but the chemicals found could also have civilian uses.
During the war, U.S. troops wore protective suits in the advance on Baghdad in anticipation of a last-ditch attack with chemical or biological weapons. None came.
Central Command attributes that to its warning that commanders ordering such an attack might face war crimes charges, and efforts by U.S. troops to knock out command and control systems that would coordinate WMD use.
In his state of the union speech in January, President Bush asserted that Iraq had biological weapons sufficient to produce over 25,000 liters of anthrax and 38,000 liters of botulinum toxin, 500 tons of sarin, mustard and VX nerve agent, and upwards of 30,000 munitions capable of delivering chemical agents.
In addition to large stockpiles of biological and chemical weapons, Iraq was accused of having missiles that exceeded the 93-mile range limit imposed after the first Gulf war. U.N. inspectors determined that Iraq's Al Samoud missile did violate that limit, and Iraq began destroying the missiles before the war began.
Central Command claims Iraq fired Al Samouds and at least one missile that violated the range limit during the war. But no Scud missiles or launchers have been reported found.
Chief United Nations weapons inspector Hans Blix this week accused the United States of dirty tricks in the run-up to war, in an interview with the BBC. Blix also says he finds it "very, very disturbing" that U.S. intelligence failed to identify as fakes some documents suggesting Iraq tried to buy uranium.
The weapons inspections chief has previously told the Spanish daily El Pais that the U.S. treated war as a forgone conclusion early in the inspection process.
Blix and some Security Council members want U.N. inspectors to return to Iraq. The United States does not support that idea. British Defense Secretary Geoff Hoon said Thursday that "independent verification" would be helpful, but indicated that either the U.N. or a third country could provide it.
U.S. officials expressed worry this week that their list of suspected WMD sites in Iraq might turn up empty, The Washington Post has reported. That could bolster the claims of war critics, who said Iraq posed no immediate threat.
It would also raise worries, even among war supporters who believed Iraq did possess illegal weapons, that the arms had been sold during the war — meaning the invasion triggered the proliferation it was intended to check.
Despite its concerns about proliferation, the Bush administration has not inventoried the stocks of civilian nuclear material at the sprawling Tuwaitha Nuclear Research Center, which it captured three weeks ago, The Post reports.
International inspectors who toured the plant in the 1990s had catalogued around 4,000 pounds of partially enriched uranium along with supplied of other radioactive materials. Some of the materials were of the kind sought by terrorists for dirty bombs.