In President Bush’s first State of the Union message, he essentially accused North Korea, Iran, and Iraq of having clandestine nuke programs and in his first enunciation of what later became known as the Bush Doctrine warned them he would "not tolerate" their having the nuke programs he accused them of having.
No matter that all three nation-states were signatories to the Nuclear Nonproliferation Treaty (NPT).
Every NPT signatory not already in possession of nukes pledges to not acquire or even seek to acquire nukes, in return for being guaranteed "inalienable" rights of access to everything "nuclear" that is peaceful.
However, all "source and special nuclear materials" as well as all activities involving the chemical or physical transformation thereof have to be "declared" and made subject to a Safeguards Agreement with the International Atomic Energy Agency.
The IAEA was created in 1957, primarily to facilitate the international transfer of nuclear energy, but the IAEA Statue requires the agency to "ensure" through its Safeguards and Physical Security regime that "adequate measures" are taken "to prevent the source and special fissionable materials" transferred or produced, subsequently, "from being used in furtherance of any military purpose."
If IAEA inspectors discover any such activity, the IAEA Board of Governors can refer the matter to the UN Security Council, which could under the UN Charter impose sanctions.
When the Treaty on Nonproliferation of Nuclear Weapons was opened for signature in 1968, the IAEA Safeguards regime with its Security Council enforcement mechanism had been in operation for more than a decade.
So the NPT simply required every signatory without nukes to enter into a IAEA Safeguards Agreement "with a view to preventing diversion of nuclear energy from peaceful uses to nuclear weapons."
Note that the NPT makes use of, but does not in any way modify, the IAEA Charter and its Safeguards regime.
However, in the aftermath of the Gulf War, the IAEA Board of Governors concluded that existing Safeguards Agreements did not ensure that adequate measures could be taken to ensure that "special fissionable materials" were not used in furtherance of some military purpose. So in 1997, the IAEA unveiled a Model Additional Protocol [.pdf], which they hoped all countries having Safeguards Agreements would accept and adhere to.
In late 2003, Iran voluntarily did sign an Additional Protocol, vastly expanding the authority of IAEA inspectors to go anywhere and see anything. In particular, under the Additional Protocol, the Iranians were required to provide all pertinent information about their plans to acquire and/or manufacture and operate gas centrifuges. Under their existing Safeguards Agreement, the Iranians had not been required to divulge any information about the planning, acquisition, or manufacture of gas centrifuges, nor any information about a future uranium-enrichment facility until shortly before introducing "source or special nuclear materials" into the centrifuges.
In other words, under the existing Iranian Safeguards Agreement, only those activities that actually involved chemical or physical transformation of source or special nuclear materials were required to be reported to the IAEA.
Since Iran began voluntarily adhering to the Additional Protocol, Director General Mohamed ElBaradei has repeatedly reported to the IAEA Board that he has found no evidence that Iran has even planned to engage in activities including those not even involving safeguarded materials in furtherance of any military purpose.
"Recalling the Director General’s assessment in GOV/2004/83 that all the declared nuclear material in Iran had been accounted for, and that such material had not been diverted to prohibited activities "
"Recognizing the right of states to the development and practical application of atomic energy for peaceful purposes, including the production of electric power "
the IAEA Board, nevertheless, expressed last week [.pdf] "serious concern" that "Iran had decided to resume the uranium conversion activities at the Uranium Conversion Facility in Esfahan."
Hadn’t those activities been subject to IAEA scrutiny for many months? And hadn’t ElBaradei found no evidence that they were doing anything at Esfahan to "further a military purpose"?
So why did the Board urge "Iran to reestablish full suspension of all enrichment related activities" at Esfahan "on the same voluntary, non-legally binding basis as requested in previous Board resolutions"?
Well, believe it or not, because after two years of go-anywhere, see-anything inspections, "the Agency is not yet in a position to conclude that there are no undeclared nuclear materials or activities in Iran."
There is nothing in the IAEA Statute that requires such a conclusion.
But even if the IAEA did come to that conclusion, do you suppose Bush would tolerate it?