"We will give all necessary cooperation to assure the world that we are not seeking to have nuclear weapons," Khatami told reporters after a cabinet meeting.
But he reiterated objections here to an IAEA ultimatum that also demands Iran stop enriching uranium.
"According to international regulations, this is our absolute right," he said, adding that the international community also "has the right to obtain assurances over the peaceful nature of our nuclear activities".
"We are ready to remove their worries," the reformist president added.
Pushed by the United States, the IAEA's board of governors on September 12 gave Iran until the end of this month to guarantee it is not developing and will not develop nuclear weapons.
The IAEA has asked Iran to produce a detailed list of its nuclear-related equipment, notably parts used in centrifuges for uranium enrichment, in order to resolve what have been described as "outstanding issues."
Much of the agency's questions are thought to revolve around the discovery on two occasions during previous inspections of traces of highly enriched uranium.
Iran asserts the traces came into the country on imported equipment, but pending a resolution of the question as well as an agreement to a tougher inspections regime, the IAEA has called on Iran to halt uranium enrichment.
On signing an additional protocol to the Non-Proliferation Treaty (NPT) -- which would allow tougher IAEA inspections -- Khatami said it had not been ruled out but left open the question of whether Iran would ever sign it.
"We have never said we would not sign the additional protocol," Khatami said, but added that Iran would "never commit itself to something that endangers national security, national interests or the integrity of the country".
"We have started negotiations on signing the additional protocol, and naturally if one day we decide to sign it, it will follow its legal course, that is to say by going through parliament," he said, although he claimed that Iran was "already implementing a large part of the protocol."
On Monday, the United States -- which has lumped Iran into an "axis of evil" along with pre-war Iraq and North Korea -- said that Iran must address all the IAEA's demands and cannot select which concerns to address.
Tehran vehemently denies Washington's accusations that it is pursuing clandestine nuclear weapons development under the cover of its civilian atomic energy programme.
A failure by Iran to meet the IAEA deadline could see it being declared in violation of the NPT and the matter being passed to the UN Security Council, which could impose sanctions as a result.