A large majority of MPs backed Mr Larijani for the influential speaker role
Iran's new parliament speaker has warned that it could set limits on future co-operation with the United Nation's nuclear agency, the IAEA.
Former nuclear negotiator Ali Larijani said parts of the agency's latest report on Tehran's nuclear programme had been "deceitful" and "ambiguous".
Mr Larijani spoke moments after being overwhelmingly voted in as speaker by the conservative-dominated parliament.
The IAEA recently voiced "serious concern" about Iran's nuclear work.
The agency's latest report, issued on Monday, said it believed Iran may be withholding information about its controversial nuclear programme.
Some countries say the programme could be used to develop nuclear weapons, while Iran says it is for entirely peaceful purposes.
Addressing parliament in a speech broadcast live on radio, Mr Larijani accused the IAEA of secretly sharing information about the Iranian nuclear file with Tehran's critics in the UN security council.
"Parliament will not allow that such deceptions are made," Mr Larijani said.
"If they continue along this path, the new parliament will intervene in the case and set a new line for co-operation with the IAEA."
The comments drew chants of "God is great" and "Death to America" from the audience of MPs.
Iran has recently been in talks with the IAEA to examine allegations it studied how to design nuclear weapons, as claimed by some member states.
The country has been put under three sets of sanctions by the UN for continuing uranium enrichment, which can be used to generate electricity or for nuclear weapons.
Correspondents say Mr Larijani's warning carries weight as he is one of the key Iranian figures in the nuclear standoff.
He served as Iran's top nuclear negotiator between 2005-2007 and he sits on the supreme national security council as representative of the Supreme Leader, Ayatollah Ali Khamenei.
Mr Larijani belongs to a group of Iranian MPs who have been critical of President Mahmoud Ahmadinejad's handling of the Iranian economy.
He won 232 votes out of a total of 263 cast in parliament for the position of speaker, Iranian news agencies reported.