British-Iraqi architect Zaha Hadid’s original design was ditched in July as estimated building costs almost doubled, reaching $2 billion.
Hakubun Shimomura said he had been asked to stay on until a planned cabinet reshuffle, but would repay some salary.
A new stadium design is due to be chosen by November.
Concerns have already been raised about whether that design will be completed in time for 2020 – the first time Tokyo has hosted the Summer Games since 1964.
As well as objections to its ballooning cost, Zaha Hadid’s design was criticized by some in Tokyo for its similarly huge size and its unusual shape.
A close ally of conservative PM Shinzo Abe, Hakubun Shimomura runs the Ministry of Education, Culture, Sports, Science and Technology, which is in charge of overseeing the Olympic Games.
Speaking at a press conference at his ministry following a meeting with the prime minister, Hakubun Shimomura said he told Shinzo Abe he wanted to take responsibility for the stadium problems.
“It is true that this has caused much concern and inconvenience,” he said.
Hakubun Shimomura added that he had first heard of the inflating costs and delays in April, “which is why I have decided to return the six months’ worth of pay I have received from that day onwards”.
His offer to quit came after an independent investigation into the fiasco.
Local reports said the panel pinned responsibility on the government body overseeing the project, the Japan Sports Council, and Hakubun Shimomura’s ministry. Former PM Yoshiro Mori, president of Tokyo’s organizing committee, was also blamed.
Plans to host the 2019 Rugby World Cup have also been thrown into doubt by the cancelation of Zaha Hadid’s original plans, as organizers now have to find an alternative final venue.
Olympic organizers are also looking for a new logo, after a Belgian artist complained that a logo he designed for a theater had been copied.
Those allegations have been denied by both Olympic organizers and the Japanese logo designer himself but he admitted his team did copy other work in the past, and the Tokyo Games committee said too many doubts had been raised for it to be used.
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