"We reject this ultimatum," Iranian ambassador Ali Akbar Salehi told the IAEA's 35-nation board of governors before storming out of a board meeting on whether to issue Tehran with an ultimatum.
The IAEA went ahead and told Iran to prove by October 31 it was not secretly developing atomic weapons.
Salehi blasted the IAEA for descending into "political dialogue" and said the ultimatum spelled "disaster" for the nuclear watchdog.
"(We) have no choice but to have a deep review of our existing level and extent of engagement with the agency," he warned, according to a copy of his speech to the IAEA board.
Salehi rejected US charges that Iran had a covert nuclear weapons program and accused Washington of entertaining "the idea of invasion of yet another territory as they aim to re-engineer and reshape the entire Middle East region."
"(The ultimatum) targets the very core of our commitments and the current course of ever-accelerating cooperation," he complained.
"For the last 24 years, Iran been subject to the most severe series of sanctions and export restrictions on material and technology for peaceful nuclear technology," Salehi continued.
"So our peaceful program had no choice but to become discreet."