Atcher, was removed from his position in October after being suspended by France's sports minister two months earlier due to alarming managerial practices.
Newspaper L'Equipe claimed on Thursday the 67-year-old was the subject of allegations of psychological harassment in the workplace.
Atcher was replaced by his deputy Julien Colette after stepping aside from the role.
"The priority of the new governance is to secure the organisation of the tournament by mobilising the necessary means for the delivery of an event to the best standards," organisers told AFP on Thursday.
It is the latest in a line of scandals to rock the competition and the sport in the country, which is one of the strongest at international and domestic level in the world.
In December, French Rugby Federation (FFR) president Bernard Laporte offered to step down from his position as he faces a suspended two-year jail sentence for corruption.
Former national team head coach and ex-sports minister Laporte decided to resign from his role as World Rugby vice-chairman following the decision, which he is appealing.
Last month, former Les Bleus forward Sebastian Chabal denied any wrongdoing following allegations he had obtained more than a hundred tickets for the World Cup thanks to his work as a competition ambassador.
Sports daily L'Equipe also claimed there were worries about the finances of the competition, which begins on September 8.
The paper claimed there was poor budgetary management, suspicions of favouritism and missappropriations of public funds.
"The Public Interest Group's (who organise the tournament) accounts were never contested during the four years Claude Atcher was general manager," Atcher told AFP later on Thursday.
A source close to France's sports minister, Amelie Oudea-Castera, told AFP there was "confidence" in the new governing team.
"We remain vigilant, alongside the FFR and World Rugby, and very attentive in respect to the operational deadlines until the delivery date of the event," they said.
World Cup organisers said they had planned to publish a new budget by the end of spring.
"It will allow a positive result at the level of the best World Cups, which will then be redistributed to French rugby," they said.
France's next game is on February 5 as they begin the defence of their Six Nations title with a trip to Italy.
