The BBC reports that the Premier League, which oversees the interests of the 20 Premiership clubs, insists "trust is lacking in the game at every level".
The League adds: "The FA board is no longer capable of properly managing its roles. The way of working is unsustainable.
"There is an underlying sense of conflict and alienation between the constituent parts of the game."
The Premier League's views have been submitted to an independent inquiry headed by Lord Terence Burns, who is conducting a review of the FA.
The report adds: "The tensions that have existed since the creation of professional football continue and there is an underlying sense of conflict and alienation.”
The League also said its clubs should feel as though they have more involvement in the England national team, which falls under the jurisdiction of the FA.
