The long-ruling supremo of amateur boxing in Japan announced his resignation Wednesday, throwing in the towel after weeks of media frenzy over a range of scandals including bout-rigging, ties to a mobster and misusing grants.

Bowing deeply at a news conference carried live on national TV, Akira Yamane apologised to Japanese boxers whose hopes of participating in the Tokyo 2020 Olympics might have been dealt a knock-out blow by his admitted ties with an underworld figure.

"I resign today," said Yamane, dubbed the "don" of Japan's amateur boxing world since he took over the federation in 2011, sporting his trademark sunglasses.

"To athletes, I apologise as the president of this body for this problem. Please, if in the future, you become unable to participate in the Tokyo Olympics, there will be the next Olympics. Please work toward that," said the 78-year-old.

In addition to the alleged misconduct, Yamane has come under intense public scrutiny for his gruff manner and snappy dress sense.

Other boxing officials have accused him of pressuring judges to favour fighters from Nara in western Japan, where he is from -- a charge Yamane denies.

He has openly admitted pressuring one boxer into sharing a public grant with two others who did not win it.

And he has acknowledged on live television his decades of friendship with the retired head of an organised crime group, asserting that they have not done anything bad together.

That argument, however, did not fly well with authorities, including Japan Sports Agency commissioner Daichi Suzuki who on Tuesday called for Yamane's resignation.