"Tehran will continue its cooperation with the IAEA despite the inappropriate resolution it adopted because we are not worried about the transparency of out peaceful nuclear activities," he said, according to the ISNA student news agency.
Khatami did not say whether Iran would accept the terms of the resolution.
IAEA inspectors began talks with Iranian officials earlier Thursday -- the last visit by staff of the United Nation's nuclear watchdog ahead of an October 31 deadline for the Islamic republic to come clean on its nuclear programme.
The organisation said in its resolution on September 12 that it wants Iran to provide clear guarantees that it is not using its civilian atomic programme as a cover for developing nuclear weapons.
It also urges Tehran to unconditionally sign, ratify and implement an additional protocol to the Non-Proliferation Treaty (NPT) allowing tougher inspections.
Iran has also been asked to cease uranium enrichment, following the discovery during previous visits by IAEA inspectors of traces of highly enriched uranium.
Tehran fiercely denies allegations that it is seeking to develop nuclear weapons, and asserts it is merely exercising its right to develop nuclear power to meet future energy needs.
Officials have also argued that the traces of enriched uranium came into the country on imported equipment.
But whether Iran will sign the protocol or meet the deadline remains a subject of intense speculation. A string of top officials have said resolution is part of a US-Israeli plot to undermine the nearly 25-year-old Islamic regime.
Later Thursday, Khatami said that in the view of Iranians "the atomic bomb is not a source of security. To have security we count on solidarity, mutual understanding, non-interference and the support of our people."