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.
The only way Blatter will not be re-elected on Wednesday is if the Congress proposes and passes a motion to call off the vote with the support of 75 percent of voting delegates.
"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."
The Scottish FA backed its English counterpart, but other national associations seemed less willing to throw their weight behind the Britons.
Allegations of cash-for-votes in the FIFA presidency campaign and the World Cup bidding process have left FIFA reeling.
Blatter, who has run FIFA since 1998, is standing unopposed after rival Mohamed bin Hammam withdrew over bribery allegations.
Earlier, the FA said an independent external party should make recommendations regarding improved governance and compliance procedures and structures throughout the FIFA decision-making processes for consideration by the full membership.
LIMITED SUPPORT
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."
The FA had already said it intended to abstain in the election for FIFA president.
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
