Ali Larijani won a landslide majority to be elelcted as parliament speaker Wednesday.
Larijani's comments came after the IAEA issued a critical report Monday that said Iran is withholding critical information that could determine whether it is trying to make nuclear weapons.
Soon after the report came out, a foreign ministry spokesman said Tehran would continue to cooperate with the agency. Larijani threw that contention into doubt Wednesday, calling the report "regrettable."
"The West must stop its strange diplomatic scheme of passing Iran's nuclear case back and forth between the U.N. Security Council and the Group 5+1," Larijani told an open session of Iran's newly-formed eighth parliament, or Majlis.
The Group 5+1 refers to the members of the U.N. Security Council plus Germany.
"The eighth Majlis will not allow such deception to go on," Larijani said, according to an account carried by state-run Press TV.
Larijani worked as Iran's nuclear negotiator from 2005 until his resignation in October 2007. His position as secretary of Iran's Supreme National Security Council gave him the responsibility of representing his country in talks with the international community concerning Iran's controversial nuclear program.
Iran insists its nuclear program is for peaceful purposes, namely energy for power lines, and in the past it has described interactions with the IAEA as positive.
But the IAEA report, dated May 26, hints at the frustrations of the IAEA investigators seeking clear answers about the program.
Iran's nuclear program has spurred concerns in the United States and much of the West. In March, after the IAEA released a similar report scrutinizing the program, the U.N. Security Council voted to impose new sanctions on Iran over its nuclear program.
