Secretary of State Condoleezza Rice said the director of national intelligence, John Negroponte, was combing through the Arabic-language material "to see whether or not there were documents there that are particularly troubling".
Ms Rice confirmed that the Pentagon website set up last March to make documents found in Iraq available to the public, had been "taken down" after concerns were raised about its content.
A New York Times article reported that officials from the International Atomic Energy Agency had complained to Washington last week about the postings of "roughly a dozen" documents from Iraq's pre-1991 nuclear research that contained diagrams, equations and other details for making a nuclear bomb.
One of the documents, running to 51 pages, covered the technical advances of Iraq's early nuclear program, including 18 pages on the development of its bomb design, materials that one expert told the Times "constitute a basic guide to building an atom bomb."
The US government created the website, called the Operation Iraqi Freedom Document Portal, in March to make available to the public a huge archive of Iraqi government papers in the hope that private experts might find useful information government translators did not have time to locate.
While many of the documents have proven innocuous, the Times said the nuclear material was identical to papers presented to the UN Security Council in 2002 in the lead-up to the US invasion.
However, the documents the Security Council saw were heavily edited to mask "sensitive information on unconventional arms," the newspaper said.
It added that a senior diplomat in Europe called the documents a "cookbook" for making a bomb.
"If you had this, it would short-circuit a lot of things," the diplomat said.
The Times said that earlier in the year UN arms control officials had complained about documents on the website that had information on producing the extremely dangerous nerve agents sarin and tabun.
The nuclear bomb papers were posted on the site in September.