EVP Kenji Simizu has been promoted to replace Minato as President.
Results of the committees investigation are expected by the end of March.
Nakai is not being investigated by police.
Fuji Television Vice Chairman Ryunosuke Endo, President Koichi Minato, Chairman Shuji Kano, and Fuji Media Holdings President Osamu Kanemitsu bowed at the beginning of a press conference todayKAZUHIRO NOGI/AFP via Getty Images
Local reports said Nakai had continued to appear on programs after execs were aware of the situation.
That didnt sit well with many companies, who immediately began pulling ads.
Nakai has denied being violent with the woman.
Reports suggest he paid her 90M($580,000) after the allegation arose.
Last week, he announced his retirement from TV and from show business.
Other networks that ran his shows have opened their own investigations to look for further wrongdoing.
