The Ministry lauded Amano’s professional activities, and extended sympathy to the Japanese government and nation, and with his family and colleagues.
Iranian Deputy Foreign Minister Seyed Abbas Araqchi also paid tribute to the head of the IAEA after his death was announced on Monday.
"My deep condolences... We worked very closely," tweeted Araqchi.
"I commend his skillful and professional performance... (that) resulted in complete closure" of the nuclear accord.
"May the Almighty bless his soul," he wrote in English.
Amano died after suffering poor health for some time, the atomic agency said.
During his tenure, Amano oversaw the signing of the 2015 nuclear deal between Tehran and world powers.
In his tweet, Araqchi noted that under Amano the IAEA had issued "15 consecutive reports confirming Iran's full compliance" with the nuclear accord.