The 83-year-old had tapped 84-year-old Saburo Kawabuchi who currently serves as the mayor of the Olympic village to take over the top position, Kawabuchi told reporters earlier.
But the choice prompted questions about whether there was not a better alternative than another older, male, and local media said Kawabuchi later turned down the job.
Local broadcaster Fuji News Network reported the government would seek to block the nomination of Kawabuchi.
“We can’t give the impression that things have changed unless we install a woman or see a generational shift,” FNN cited a government source as saying.
The Mori controversy has done “serious reputation damage” to the Tokyo Olympics, and the selection of Kawabuchi is far short of restoring the trust, said one source involved in the Olympics.
The source, requesting anonymity due to the sensitivity of the matter, said many officials wanted a woman to replace Mori.
Local media said the country’s Olympics Minister, Seiko Hashimoto, was being considered as a possible candidate.
Prime Minister Yoshihide Suga had asked Mori if there was either a younger or a female candidate to succeed, but Mori recommended Kawabuchi.
Top government spokesman Katsunobu Kato said he was not aware of Suga’s conversation with Mori.
The Tokyo Olympics organising committee declined to comment on media reports over Mori and Kawabuchi.
Later on Friday, the organising committee plans to hold a meeting of its council and executive board, followed by a press conference.
Mori will explain his position at Friday’s Games meeting, Japanese Olympics Minister Seiko Hashimoto told parliament, referring to a phone call with Mori.
Asked whether it is possible for Mori, a departing leader, to appoint his own successor, Hashimoto said there needs to be proper procedures to pick the next leader for the organising committee.
Mori’s resignation less than six months before the Summer Olympics are scheduled to begin is likely to raise new doubts over the viability of holding the postponed Games during a pandemic.