England, with the support of neighbours Scotland, will propose during Congress that the election of the 75-year-old Swiss, the sole candidate, should be delayed after a corruption scandal raised concerns about his leadership of soccer.
Bernstein told a news briefing during the opening ceremony of the Congress that the proposal was a matter of principle.
"To get the 150-odd votes we need clearly would be extremely difficult when we are starting from a standing start," he said.
"But there was actually a matter of principle involved. Myself and the FA feel that the situation FIFA has got itself into is, in many ways, unacceptable.
"My board decided to abstain from the election when there were two candidates standing, now there is only one left and, given all the issues that have emerged since we did so, it would have been inconsistent to have supported a one-horse race candidate," added Bernstein.
"I don't think it would have been in the interests of anybody, nor may I say in the interests of Mr Blatter.
"I would have thought if he's going to continue he should want to continue having won a proper election with opposition and then go forward with a full mandate," added Bernstein.
"Going forward in this situation if he does with a coronation rather than an election I don't think does anybody any good."
Asked if the FA had enough support, he said: "What I do know is there is a lot of latent support, a lot of passive support, but whether that will translate itself into people putting their heads above the parapet we will see."
FA President Prince William was "fully supportive" of Bernstein and the proposals, a St. James's Palace spokesperson told the BBC.
"He considers the transparency of the international governing body to be integral to the good governance of the game."
England's relations with FIFA have been strained since it failed in a bid to host the 2018 World Cup despite a campaign featuring Prime Minister Da
