"I hope he will work hard to fulfil the role of the IAEA to achieve non-proliferation."
The mayor of Hiroshima, the southwestern city that suffered the first nuclear attack in 1945, was also among those offering congratulatory messages on Friday.
Amano's appointment follows a narrow win over his South African rival Abdul Samad Minty in a ballot of IAEA board members in Vienna on Thursday, and it is not without controversy.
While several industrialised nations on the board gave the Japanese their backing, other countries had voiced concern about his ability to tackle rising threats to global non-proliferation and his support for a tough approach on Iran's disputed nuclear programme.
Many nations had wanted an IAEA leader with broad support and, according to an EU diplomat, Russia had told other board members that it would be "unacceptable" if Amano were elected by only the minimum winning margin of two-thirds – exactly what Amano received.
Moreover, there has been some scepticism over Tokyo's vow to never make or own nuclear weapons, given its widespread nuclear energy programme and huge supplies of uranium and plutonium, which could potentially be used to make weapons.
North Korea's recent nuclear tests have raised speculation that Japan, if it feels sufficiently threatened, could move to develop its own nuclear weapons.
Amano will be taking control of the nuclear inspectorate at a particularly difficult time.
Its investigations into Iran and Syria are deadlocked and its inspectors were kicked out of North Korea following the UN's condemnation of a rocket launch in April.
North Korea says the launch placed a satellite into orbit but critics say was a cover for a long-range ballistic missile test.
On top of those challenges, Amano will also have to persuade the 35 member countries to contribute more money to the agency's budget.