The president of one of Japan’s most influential entertainment agencies resigned after an independent investigation confirmed the company’s founder, Johnny Kitagawa, had sexually abused young men in his care since the 1970s.

Allegations against Mr. Kitagawa, who helped aspirants achieve pop stardom in Japan, have circulated for decades, but were largely ignored by a quiescent media that had become dependent on the entertainment mogul and his family-run company, Johnny & Associates, to provide access to the young performers. His reputation as a hitmaker associated with some of Japan’s most popular boy bands protected Mr. Kitagawa from scandal, even after his death in 2019 at age 87.

The release of an hourlong BBC documentary in March featuring interviews with three of Mr. Kitagawa’s accusers opened a floodgate of recrimination, prompting more men to come forward and putting pressure on the company to respond. Under immense scrutiny, Johnny & Associates announced in May that it was forming an internal investigative panel to “prevent the recurrence” of future abuse.

At a news conference on Thursday, Julie Keiko Fujishima, Mr. Kitagawa’s niece, acknowledged the results of the investigation and apologized on behalf of herself and the company. She also announced she had resigned as the company’s president on Wednesday.

“These problems were caused by my uncle, and, as his niece, I want to take responsibility for them,” she said, adding that the company would seek to offer support and compensation to accusers. (Ms. Fujishima, the company’s sole owner, will remain as a board member, responsible solely for relief and compensation.)

The report, released in late August, confirmed hundreds of cases of abuse by Mr. Kitagawa going back more than 50 years. It cited a lack of corporate governance at the company and media complicity as major factors in his impunity. Mr. Kitagawa’s sister, Mary, who died in 2021, also played a role in covering up his behavior and protecting him from the consequences, the report concluded.

No criminal charges were ever filed against Mr. Kitagawa, who consistently denied the accusations against him.

Ms. Fujishima, who has served on the company’s board since 1998 and was appointed president in 2019, said that she had no direct knowledge of Mr. Kitagawa’s behavior and had little personal interaction with performers represented by the agency before his death.

She had been aware of allegations against him, she said, but at the time “couldn’t imagine taking any action.”

Ms. Fujishima will be replaced by Noriyuki Higashiyama, a singer who rose to fame under the auspices of Johnny & Associates and later became a successful actor and news anchor.

Mr. Higashiyama said that he had not been sexually abused by Mr. Kitagawa and had not known that it was happening to others, although he had heard rumors. In comments on Thursday, he pledged to reform the company.

“I believed Mr. Kitagawa,” he said, describing the mogul as a father figure.

Speaking at a parallel news conference, Kazuya Nakamura, who has accused Mr. Kitagawa of abusing him while he was an aspiring performer, said that the company’s admission of guilt “felt like a dream.”

But he questioned the company’s sincerity and suggested that appointing Mr. Higashiyama, who was one of Mr. Kitagawa’s top stars during the time of the abuse, made it difficult to believe that the company was committed to change.

Some of Mr. Kitagawa’s accusers have said that they are considering filing civil and criminal complaints against the company in Japan and civil suits overseas, where they have alleged some of the abuse occurred.

In his heyday, Mr. Kitagawa was regarded as the king of Japanese boy bands, creating more than a dozen power groups that dominated the J-Pop music scene. Boys as young as 9 were recruited by Mr. Kitagawa and lived together in a dormitory, where they were trained to sing, dance and conduct themselves like pop idols.

The company continues to manage some of Japan’s most popular musical acts, with considerable influence and power in the entertainment industry. It will keep its name for now, Mr. Higashiyama said Thursday.

Rumors about Mr. Kitagawa’s behavior first came to public attention in 1999, when the weekly tabloid Shukan Bunshun wrote about the experiences of several anonymous men. But other news outlets largely ignored the story, and Mr. Kitagawa won a libel suit against Shukan Bunshun’s publisher. Damages of 8.8 million yen (about $60,000) were later reduced on appeal.