Iran's supreme leader Ayatollah Ali Khamenei earlier ruled out inspections at the country’s military sites.
But IAEA head Yukiya Amano told AFP on Tuesday that Tehran had agreed to implementing the Additional Protocol of the Nuclear Non-Proliferation Treaty (NPT) that allows for snap inspections of its nuclear facilities, and if required, military sites.
However, Iran appears to be interpreting the protocol differently, with Foreign Minister Mohammad Javad Zarif arguing that the protocol allows "some access" but not inspections of military sites, in order to protect national "military or economic secrets.”
Iran and the P5+1 group of international mediators have been engaged for nearly two years in negotiations on Tehran's nuclear program.
The deal is aimed at preventing Iran from developing a nuclear weapon in exchange for an easing of hard-hitting economic sanctions.
The two sides signed a framework agreement on April 2 and began meeting in Vienna on Wednesday to put finishing touches to the deal which is due by June 30.