"The FA Board has today agreed to abstain in the vote for the Presidency of FIFA," the FA said in a statement on Thursday ahead of the June 1 vote.
"There are a well-reported range of issues both recent and current which, in the view of The FA board, make it difficult to support either candidate."
The FA were left aghast by FIFA's executive committee after being comprehensively beaten in the race to host the 2018 World Cup.
After attracting only two votes, one of them its own, FA officials and bid representatives said that potential voters had lied to them and that the voting system was flawed. Russia won the bid.
"The FA values its relationships with its international football partners extremely highly. We are determined to play an active and influential role through our representation within both UEFA and FIFA," the statement added.
"We will continue to work hard to bring about any changes we think would benefit all of international football."
Former FA chairman David Triesman told a UK parliamentary inquiry last week that the 2018 bid process was stained by corruption.
The inquiry also heard that Qatar's successful bid to host the 2022 tournament, backed by Asia confederation president Bin Hammam, a Qatari, was also marred by allegations of wrongdoing.
UK member of parliament Damian Collins said there was evidence from the Sunday Times newspaper that executive committee members Issa Hayatou of Cameroon and Jacques Anouma of the Ivory Coast were paid by Qatar.
"BIT STRANGE"
Qatar and the duo have denied the allegations while the FA have appointed a barrister to lead an independent inquiry into Triesman's accusations.
FIFA, who suspended two executive committee members from voting on the 2018 and 2022 World Cups following earlier allegations that they had offered to sell their votes, is also to hold an investigation.
Blatter, before the FA officially announced it would abstain), said it was a "little bit strange when the number one association in the world" cannot decide.
"The FA have two candidates in front of them and cannot make a decision which one to support," he told reporters.
"Of course, you can abstain but I explained to (FA chairman David) Bernstein the part FA has played in the development of football, specifically in the laws of the game, having organised FIFA and modern football.
"He (Bernstein) asked me what FIFA can do for England and I put it the other way - what can England do for FIFA? With their efficient Premier League, they should ask what can we do for FIFA?"
Blatter earlier announced that FIFA will interview an unidentified whistleblower at the centre of the newspaper allegations concerning Qatar.
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