They have been blocked, however, from returning to investigate suspicions that explosive tests were carried out related to possible nuclear triggers. Iran denies the allegations, but has resisted opening the base.
It was unclear whether the openings made Monday would eventually extend to sites such as Parchin.
Amano said it would be “raised in subsequent” meetings.
Iran's nuclear chief, Ali Akbar Salehi, said the pact is intended as “a roadmap that clarifies the mutual steps required for resolving the outstanding issues”—points repeatedly raised by President Hassan Rouhani since taking office in August.
A joint statement by Salehi and Amano said both sides seek to “cooperate further ... to resolve all present and past issues.” The IAEA, in a nod to Iran's concerns, also agreed to protect confidential information regarding its nuclear program.