The agency (IAEA) has not lived up to its obligations, Rafsanjani, who currently chairs the State Expediency Council, said at a conference in Tehran.
Rafsanjani said that the United Nations nuclear agency had failed to support countries in developing nuclear energy.
The top cleric also claimed the IAEA had given the bullying powers an excuse to put pressure on Tehran over its sensitive nuclear work.
In March, the Security Council adopted a Presidential Statement unanimously giving Iran until April 28 to suspend all of its uranium enrichment activities and resume its cooperation with the UN nuclear watchdog.
Irans hard-line President has since said that Tehran would never abandon its right to uranium enrichment.