The question of inspections is shaping up to be one of the thorniest issues as world powers try to finalise a deal by June 30 to prevent Iran from developing a nuclear bomb.
Amano said Tehran has 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, differences have emerged over the interpretation of the protocol and the issue is far from resolved.
And Foreign Minister Mohammad Javad Zarif has said the protocol allows "some access" but not inspections of military sites, in order to protect national "military or economic secrets".
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In an interview with AFP and French daily Le Monde, Amano said that if a deal is reached, Iran will face the same inspections from the International Atomic Energy Agency (IAEA) as any of the 120 countries implementing the additional protocol.
"When we find inconsistency or when we have doubts we can request access to the undeclared location for example, and this could include military sites," said the Japanese diplomat.
Iran and the so-called P5+1 group -- Britain, China, France, Russia, the United States plus Germany -- have been engaged for nearly two years in negotiations on Tehran's nuclear drive.
The deal is aimed at preventing Iran from developing the atomic bomb in exchange for an easing of crippling economic sanctions.
The two sides signed a framework agreement on April 2 and began meeting in Vienna on Wednesday to start finalising a deal which is due by June 30.
According to the United States, Iran has agreed to cut the number of its centrifuges, used for enriching uranium, by two thirds from 19,000 to about 6,000, and will put excess nuclear equipment into storage monitored by the IAEA.