"We will only accept the legal controls of the IAEA within the framework of the Non-Proliferation Treaty," the president said during a visit by International Atomic Energy Agency chief Yukiya Amano.
"Any monitoring beyond those rules would be a precedent, against the interests of all developing countries," Rouhani said.
Amano made a one-day visit to Tehran ahead of an August 25 deadline for Iran to answer decade-old allegations of past nuclear weapons research.
He held morning talks with Foreign Minister Mohammad Javad Zarif before meeting Rouhani, Iran's official IRNA news agency reported. He later also met with Ali Akbar Salehi, head of the Iranian Atomic Energy Organisation.
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The submissions were in response to a November 2011 IAEA report that it had intelligence that Iran had until 2003 and possibly since then conducted research into developing nuclear weapons.
Addressing these claims, long refuted by Iran, would be an important element in the comprehensive accord over Tehran's nuclear programme that Iran and world powers want to strike by November 24.
Amano had said in a May report that Iran showed information to the agency that "simultaneous firing of EBW (Explosive Bridge Wire detonators) was tested for a civilian application".
At a press conference today in Tehran, Amano broached the issue again, saying Iran had provided information and explanations to the IAEA on Tehran's decision, in early 2000, to develop safer detonators.
"Iran has also provided information and explanations to the (IAEA) on its work post-2007 related to the application of EBWs in the oil and gas industry which is not inconsistent with specialised industry practices," he added.
Amano in his talks with Rouhani today said he hoped "cooperation will continue in this more constructive atmosphere".