Addressing parliament just after his election, Larijani expressed regret that in its latest report on the Iranian nuclear drive the International Atomic Energy Agency (IAEA) had "spoken in an ambiguous way."
"This was used by the media, as you have seen, in the last days. This attitude of the agency is regrettable," he said in the speech broadcast live on state radio.
"Parliament will not allow that such deceptions are made and if they continue along this path, the new parliament will intervene in the case and set a new line for cooperation with the IAEA."
In the report, the IAEA expressed "serious concern" that Iran was still hiding information about alleged studies into making nuclear warheads and defying UN demands to suspend uranium enrichment.
Observers said the report marked a tougher line from the IAEA, which has conducted four years of investigations into the Iranian nuclear drive but has never drawn a conclusion over its nature.
Larijani warned the IAEA that if its reports were not more "balanced" in the future it would harm cooperation between them.
"If they want a more sincere cooperation with Iran they need to have more balanced reports and not look to create a media frenzy."
The United States and its European allies fear Iran wants to use the sensitive process of uranium enrichment to make an atomic weapon.
Tehran insists its drive is entirely peaceful.
Iran has in recent weeks held talks with the IAEA to examine the allegations that Tehran has studied how to design nuclear weapons. The claims stem from intelligence provided to the IAEA by some member states.
They were first presented at a closed-door briefing to diplomats at IAEA headquarters in Vienna on February 25 by its deputy director general Olli Heinonen.
Washington and its allies responded immediately to the new IAEA report, saying it underlined international concerns about the aims of the Iranian nuclear programme.
"There are a number of different questions out there about the military's involvement in this nuclear programme, about Iran's efforts to fabricate hemispheres of uranium," US State Department spokesman Sean McCormack said.
"And I'm not sure other than for a weapon why you would do that," McCormack added.
In Berlin, German Foreign Minister Frank-Walter Steinmeier said the report "leaves open a number of questions that we will have to examine very quickly."
Larijani's warning carries weight as its comes from one of the key Iranian figures in the nuclear standoff.
He served as top nuclear negotiator between 2005-2007, holding several rounds of talks with the European Union, before resigning due to differences with President Mahmoud Ahmadinejad.
Even before his election to the powerful post of speaker, he retained an influence on nuclear policy as the representative on Iran's supreme national security council of supreme leader Ayatollah Ali Khamenei.
