The news followed an urgent meeting of the FFF executive committee.
Le Graet has been in the firing line over allegations of sexual harassment which he denies and criticism of French soccer icon and 1998 World Cup winner Zinedine Zidane (50), which drew the ire of players and politicians.
Work will now begin on the election of a new president and the review of several decisions taken by Noel Le Graet, notably the renewal of Didier Deschamps' contract for another three and a half years without the approval of the FFF executive committee.
The FFF added that the contract has been validated by the executive committee on Wednesday.
Le Graet, the former mayor of Guingamp and ex-president of the western town's football club that under his guidance won the 2009 French Cup, took office in 2011.
The FFF added that general director Florence Hardouin was 'provisionally suspended', with Diallo also taking charge of her role on an interim basis.
Last September, the Sports ministry ordered an audit of the federation the FFF said it would file a defamation lawsuit against So Foot magazine, which reported that Le Graet allegedly harassed several female employees.