According to the New York Times IAEA head Amano has "asserted a right" to investigate Iran's missile program because it could be related to nuclear weapons. He has also repeated the mantra that the IAEA cannot verify the exclusively peaceful nature of Iran's nuclear program because there could be undeclared nuclear facilities.
On the first point, he's is just plain wrong. Read the text of Iran's safeguards agreement with the IAEA, specifically Article 19 which states that he IAEA may refer Iran to the UN Security Council ONLY if the IAEA is "not able to verify that there has been no diversion of nuclear material required to be safeguarded under this Agreement, to nuclear weapons or other nuclear explosive devices" and Art. 2 which states that the purpose of the safeguards agreement is for the "exclusive purpose of verifying that such material is not diverted to nuclear weapons or other nuclear explosive devices." (emphasis mine.)
The IAEA has repeatedly and consistently stated that there has been no diversion of nuclear material in Iran in every single report it has issued. The Feb 2008 IAEA report also explicitly states that it has no evidence that any of the "alleged studies" into making nuclear warheads and missiles by Iran involved a diversion of nuclear material, and that the IAEA has "no credible information in that regard" either. This language is not in the report without a reason -- it points to a very signficant legal issue explained further in paragraph 52 of the Feb 2006 IAEA report on Iran:
“[A]bsent some nexus to nuclear material the Agency’s legal authority to pursue the verification of possible nuclear weapons related activity is limited.”
In other words the IAEA does not have a carte blanche for inspectors to go poking around everywhere in a country and demanding access to missile or other weapons programs. Rather, the application of safeguards is limited to the monitoring of nuclear material to ensure that "significant quantities" of such material is not secretly diverted to non-peaceful uses. This monitoring is accomplished through systematic inspections, surveillance and accounting for nuclear material as specified in the country's safeguards agreement -- all of which been duly performed in Iran with no evidence of any nuclear weapons found -- but even then such measures are supposed to be carried out with great deference to a country's sovereignty. For example, the IAEA's model safeguards agreement (INFCIRC-153) imposes various limits on the man-hours of inspections, and requires that IAEA inspections avoid hampering or causing "undue inteference" with civilian nuclear programs, whilst also requiring that the IAEA collects the “minimum amount of information and data consistent with carrying out its responsibilities” and “reduce to a minimum the possible inconvenience and disturbance to the State.”
On the second point -- whether Iran's nuclear program is "exclusively peaceful" -- the IAEA does not verify the exclusively peaceful nature of ANY country's nuclear program unless they have signed and ratified the Additional Protocol. Most countries have flatly refused to do so, though Iran has signed and had voluntarily implemented it for more than two years without ratification, and has offered to permanently implement it if it's nuclear right are also recognized. So the next time Amano says that he can't verify the exclusively peaceful nature of Iran's nuclear program, someone should ask him if he can verify the exclusively peaceful nature of Egypt's, S. Korea's, Argentina's or Brazil's nuclear program.
Amano's won the election to head the IAEA by a single vote over the requisite two-thirds majority after a bitter and protracted division in the IAEA Board between the developing countries who supported Samad Minty, a South African nuclear diplomat who was intensely opposed by most advanced nuclear members, and developed countries such as the United States and the EU who supported Amano, a career diplomat not known for taking risks or assuming a high profile.
The Western press has lauded Amano for having “broken with the more cautious style of his predecessor, Mohamed ElBaradei” who had been elected unanimously back in 1997. Elbaradei was labelled as being "cautious" only because of his refusal to go along with the hyperbolic claims of the Bush administration about Iran and Iraq. ElBaradei's deep disagreements with the United States about the Iraq War and the Iranian nuclear program brought him into direct conflict with the Bush administration, which eventually even resorted to clandestinely tapping his telephone in order to force him out of office. The criticism of Elbaradei by the United States and Israel (whose officials had openly accused ElBaradei of being "pro-Iranian") reached a pitch when in August 2007, Iran and the IAEA agreed to a “work plan” to address outstanding issues with respect to Iran's nuclear program, and when in Feb 2008 the IAEA issued a report which concluded that Iran had addressed all outstanding issues regarding its uranium enrichment program and so there were "no other remaining issues and ambiguities regarding Iran’s past nuclear program and activities."
With the departure of ElBaradei as the head of the IAEA, a deep and bitter divide has opened up on the IAEA Board of Governors between advanced nuclear states, including most of the states with nuclear weapons, and developing countries that make up a majority of the membership. On highly publicized issues such as Iran and Syria, consensus has evaporated.
It remains to be seen whether Amano can restore consensus to the IAEA Board and ebuilding trust particularly of the majority of its members who represent the developing countries. However, his perfomance with respect to Iran thus far does not bode well.
[Note: Even if Iran was subject to the requirements of the Additional Protocol, the IAEA would still not have a right to investigate Iran's missile program. The Additional Protocol allows more intrusive inspections of nuclear facilities and facilties related to the nuclear fuel cycle, not other weapons facilities absent some evidence that the other weapons programs actually involved nuclear material -- which the IAEA has explicitly said is not the case with respect to the "alleged studies" by Iran.
Note further that even under Iran's existing safeguards agreement, if the US has evidence to suspect that Iran has illicit, undeclared nuclear facilities and activities, it can provide the evidence to the IAEA Board of Governors which is entitled to then demand "special inspections" -- however this has never happened and the United States has not fully provided the "alleged studies" evidence to the IAEA, though Iran is expected nevertheless to somehow refute the claims allegedly contained in documents that the US has not permitted the IAEA to share with Iran.