Japan must first address its treatment of refugees and other humanitarian violations such as human trafficking and the death penalty.
At a meeting with top Japanese government officials in Tokyo on Thursday, Irene Zubaida Khan said she would be "prodding" to bring improvements to Japan's human-rights record.
"With its initiative for reform of the UN and the strong bid for a Security Council seat, this is Japan's opportunity to promote itself as a leader in terms of global human rights," she said, adding that Amnesty considers human rights to be central to the concept of wider security.
"Japan is one of only two industrialised countries with the death penalty, along with the United States, and while we see movement in the US and there is an international trend of more countries abolishing the death penalty or not using it, 42 people were sentenced to death in Japan last year," Khan told Aljazeera.net.
Amnesty International: Japan
must improve its rights record
"We want Japan to look at this not only because it's a cruel and inhumane punishment, but also because of the possibility of miscarriages of justice due to the use of confession-based convictions," she said.
Khan is the first woman and first Muslim to head the London-based human-rights organisation.
She criticised Tokyo's attitude towards asylum-seekers, pointing out that of the 426 applications last year for refugee status, just 15 people were given permission to remain in Japan, while she added that victims of human trafficking need support and protection rather than deportation.
"Japan is in a neighbourhood that has some major human-rights concerns, with China, North Korea and Indonesia all nearby, and we want Japan to play a more proactive human rights role in Asia," Khan said.
Not good enough
Bush has dismissed Amnesty
International's criticism of US
"By bidding for the UNSC seat, Japan is subjecting itself to closer international scrutiny and while Japan has made it clear that it is concerned about its refugee situation, we would say that the improvements it is making are good but are not enough," Khan said.
"I'm trying to explain to officials the new dynamic that the bid for the UN permanent seat adds," she added.
Khan's visit to Japan comes just days after the release of Amnesty's annual report on the state of global human rights, which has been called "absurd" by President George Bush's administration.
Khan told Aljazeera.net, Amnesty International is open to international scrutiny and that the US must also be scrutinised when it comes to its human-rights record.