Mr Amano had led the Vienna-based UN agency since 2009, and was due to step down in March 2020 because of an unspecified illness.
The Japanese national took over from Mohamed ElBaradei a decade ago and his third term was due to run until November 2021.
Mr Amano served as chair of the agency’s board of governors from September 2005 to September 2006. He was Japan’s resident representative to the agency from 2005 until his election as director-general in July 2009.
At the Japanese foreign ministry, Mr Amano was director-general for the disarmament, non-proliferation and science department from 2002 until 2005.
According to the BBC, Mr Amano appeared increasingly frail in recent months after undergoing an unspecified medical procedure in September.
His death coincides with a sharp escalation of tensions between Iran and the West following Washington’s decision last year to quit a 2015 international deal that curbed Tehran’s nuclear programme in return for an easing of economic sanctions. The 2015 deal is policed by the IAEA.
Today’s IAEA statement did not give any schedule for naming a successor.
“The Secretariat is in communication with board members,” an IAEA spokesman said in a separate statement.
Mary Alice Hayward, deputy director-general and head of the department of management, is now the acting director-general, the spokesman added.
“The Secretariat of the International Atomic Energy Agency regrets to inform with deepest sadness of the passing away of Director General Yukiya Amano,” the IAEA statement said.
The Secretariat said it wishes to share Mr Amano’s most recent reflection which he intended to include in his letter to the Board of Governors announcing his decision to step down:
“During the past decade, the Agency delivered concrete results to achieve the objective of ‘Atoms for Peace and Development’, thanks to the support of Member States and the dedication of Agency staff. I am very proud of our achievements, and grateful to Member States and Agency staff.”
The agency said the flag over its head office in Vienna had been lowered to half-mast