An official of the country that drew up the report was reported as telling AP that "elements" referred to state employees acting on their own without approval of the Kazakh government.
In response to questions about the report, a Kazakh official told the AFP news agency that it complied fully with international law and IAEA rules.
"We need to study this carefully, formulate all the arguments and provide a reasonable answer," Yerzhan Ashikbayev, the Kazakh foreign ministry spokesman, said.
There was no immediate comment from Iran.
Purified ore, or uranium oxide, known as yellowcake, is processed into a uranium gas, which is then spun and respun to varying degrees of enrichment.
Low enriched uranium is used for nuclear fuel, and upper-end high enriched uranium for nuclear weapons.
Commenting on the leaked intelligence report, Ian Kelly, the US state department spokesman, said "the transfer of any uranium yellowcake ... to Iran would constitute a clear violation of UNSC sanctions".
"We have been engaged with many of our international nonproliferation partners on Iran's illicit efforts to acquire new supplies of uranium over the past several years," he said.
Iran has already been hit with three rounds of UN sanctions over its failure to meet UN demands that it halt its controversial nuclear enrichment programme.
Under those sanctions, Iran is banned from importing all items, materials, equipment, goods and technology that could contribute to its enrichment activities.
The US and its allies say that Iran is seeking to use the programme to build nuclear weapons, but Tehran says it is a civilian programme designed to meet its energy needs.
Iran has effectively dismissed the end of the year deadline for it to accept a deal that would see low-enriched fuel sent abroad in exchange for processed fuel for its nuclear reactors.
The US and allies on the UN Security Council are now reportedly considering a new round of sanctions that would target Iranian leaders and the powerful Revolutionary Guard, due to concerns that sweeping restrictions would not garner international support.
US state department spokesman Kelly said the administration wanted to "ensure that any legislation that emerges preserves the necessary flexibility to pursue the president's policy".
The IAEA believes that Iran's enrichment programme has been built on 600 tons of uranium oxide imported from South Africa during the 1970s as part of plans by the pre-revolution leadership to build a network of nuclear reactors.
The Washington-based Institute for Science and International Security said earlier this year that, based on 2008 IAEA statistics, Iran had already used up close to three-quarters of its South African supply.
In a November report, the IAEA noted that Iran had stopped producing uranium gas from yellowcake in early August and said Iranian officials had notified the agency that the production facility was down for maintenance.
Kazakhstan is among the world's three top producers of uranium, accounting for more than 8,500 tons last year.
Iran, in contrast, is producing an estimated 20 tons a year, too little to power even one large reactor let alone the network it says it wants to put in place.