The tripartite meeting would be between Iranian Foreign Minister Abbas Araghchi, his Egyptian counterpart Badr Abdelatty and IAEA chief Rafael Grossi, the ministry said in a statement.
It comes a day after a report by the UN agency showed Iran has stepped up production of uranium enriched up to 60 percent -- close to the roughly 90 percent level needed for atomic weapons.
The UN report was leaked as Iran holds talks with the United States on its nuclear programme, after Washington unilaterally abandoned a landmark agreement between Tehran and world powers in 2018 during President Donald Trump's first term.
The 2015 deal, known as the Joint Comprehensive Plan of Action, aimed to stop Iran from developing a nuclear bomb -- a goal Western countries accused it of pursuing, though Tehran denies it.
During his visit to Cairo, Araghchi was also scheduled to meet Egyptian President Abdel Fattah al-Sisi, Iran's Tasnim news agency reported.
The Iranian minister said on Saturday that he had received "elements" of a US proposal for a potential nuclear deal following five rounds of talks mediated by Oman.
Araghchi said he spoke to Grossi in a phone call on Sunday, warning against possible European sanctions.
He urged the IAEA chief to stop "parties from exploiting" the nuclear watchdog report "to advance their political objectives".
The UN agency's board of governors is set to review Iran's nuclear activities in its upcoming quarterly meeting in Vienna starting June 9, reports BSS.