"The Islamic Republic of Iran has had extensive relations with the IAEA in the past 12 years and has always tried to keep these ties good, regular and legal," Rouhani said during the meeting in Tehran on Sunday.
"We hope that by acting upon its responsibilities, the IAEA would move more in the next few months to help the scientific progress of countries, including Iran," he added.
Rouhani referred to the nuclear agreement clinched between Tehran and the world powers in Vienna on July 14, and said, "While implementing the Joint Comprehensive Plan of Action (JCPOA), we will implement the Additional Protocol (to the Non-Proliferation Treaty (NPT)) voluntarily and we hope that you will also fairly supervise the implementation of the JCPOA."
Stressing Iran's close cooperation with the IAEA, he said, "Fortunately, the truth about Iran's peaceful nuclear activities in the past few years has been proved by the IAEA supervisions and snap inspections and it has been emphasized that Iran has never had any diversion in its peaceful program."
Amano traveled to Tehran on Sunday to hold talks with Head of the Atomic Energy Organization of Iran (AEOI) Ali Akbar Salehi and other Iranian officials on ways to implement a cooperation roadmap plan signed between Tehran and the IAEA in July.
Amano and Salehi signed a roadmap of cooperation in Vienna on July 14.
The roadmap contains secret arrangements stated in one or two documents entailing on the methods to be used by the two sides in their cooperation.
Senior Iranian nuclear officials have said that all IAEA member states have such secret agreements and the UN nuclear watchdog is duty bound to keep them secret to any third party individual or state.
After the roadmap was signed, Salehi announced that the new agreement would fully settle all unresolved issues pertaining to Tehran's nuclear activities in the past.
"All past issues will be resolved completely after Iran and the Agency adopt some measures," Salehi told reporters after signing an agreement called the Iran-IAEA Cooperation 'Roadmap'.
He said that all agreements, including the measures decided for Parchin military site, will be implemented with full respect to Iran's redlines.
Iran had earlier announced that inspection of the country's military sites are one of its redlines.
"I hope that a new chapter in relations and cooperation between Iran and the IAEA will start after the settlement of the past issues," Salehi added.
Salehi made the remarks in Vienna just a short time after diplomats acknowledged a sum-up agreement had been made between world powers and Iran; FNA reported.