Welsh Rugby Union (WRU) chief executive Steve Phillips resigned on Sunday after allegations were made of a "toxic culture" at the governing body.
Phillips stepped down after a turbulent week for the sport in Wales following a BBC documentary that aired allegations of sexism, racism and homophobia at the WRU.
Former Olympic hurdler and Wales wing Nigel Walker was named as caretaker CEO, and he warned of an "existential crisis" for Welsh rugby.
"It is with a huge amount of regret that I have decided to hand in my resignation," Phillips said in a statement issued by the WRU.
"I have always had the best interests of Welsh rugby at the heart of my every action and thought, but have come to the conclusion that it is now time for someone else to lead the way."
In the documentary, shown last week, former general manager for women's rugby Charlotte Wathan spoke of how a male colleague had said in front of others that he wanted to "rape" her and that she had considered suicide due to what she described as a "toxic culture" of sexism at the WRU.
Another unnamed contributor said she was left contemplating suicide by her experiences of bullying and sexism at work.
"No allegations were made against Steve Phillips in the recent BBC programme and he was not accused of any wrongdoing," the WRU statement said.
The four Welsh regional clubs - Cardiff, Dragons, Ospreys and Scarlets - had backed calls for the 58-year-old Phillips and the WRU board to resign.
The Welsh Rugby Players Association said on Friday it was "appalled by the allegations" and called for the "strongest possible action".
Walker, who won 17 caps in the 1990s, was brought in by Phillips as performance director in July 2021 and now steps up to interim CEO.
"There is no doubt that Welsh rugby is facing an existential crisis," he said.
"This has been a wake-up call. Perhaps it is a call that has been overdue. The first step to any recovery is admitting the problem.
"We must now listen intently to what people from outside our organisation are telling us."
Walker said the organisation was "committed to equality, diversity and inclusion" but needed "to do better."
WRU chairperson Ieuan Evans, who last week said Phillips had a role to play in the future of Welsh rugby, on Sunday praised him for taking the decision to step down.
"We've always been in constant contact and we came to the conclusion that we needed a fresh perspective and leadership to move forward," he told BBC Wales.
Evans, who has committed to an external taskforce to tackle the issues, has vowed to stay in his post.
The former Wales great, who only took over from Rob Butcher in November, said he needed to lead changes alongside Walker.
"We have already started the process with the Welsh government and Sport Wales in establishing an independent taskforce," he told BBC Wales.
"It's now for me as chair of the board and chair of the Welsh Rugby Union to... drive those changes."
Wales launch their Six Nations campaign at home to Ireland on Saturday.