The guidelines, which were brought in late last year, in effect to end offside for players who do not touch the ball or directly block the vision or movement of an opponent.
Bolton, who drew 1-1 at Leicester City in the premier league on Tuesday, utilised the guidelines to maximum effect from set-pieces and netted their equaliser from one such move.
The English League Cup finalists employed two unmarked players standing in "offside" positions close to Leicester goalkeeper Ian Walker before running away from goal as a free kick was fired into the penalty area.
The move caused enough consternation for Walker, who complained the players had got in his field of vision, to lose concentration and spill a shot from Kevin Davies, palming the ball back under his body and into the net.
"I think they (FIFA) have got it horribly wrong. There is obviously nothing I can do about it apart from try use it to my advantage," said Allardyce.
"I don't like it, I don't think it adds anything to the game whatsoever other than confusion."
"It's not the referees fault, it's FIFA's. Hopefully they may change it back."
CHAOTIC SCENES
The guidelines were issued in a circular to national football federations and while they are not a rule change, they are more precise saying that offside for "interfering with play" means "playing or touching a ball passed or touched by a team mate".
Allardyce said the guidelines could lead to chaotic scenes on the pitch.
"What we are going to get sooner or later is 22 players in the six-yard box when a free kick comes in and that is just not adding to the spirit of the game.
"I think probably the referees don't like it, The (English) FA should have a look at it and put our case forward and try and get back to some common sense."
"What we have done today doesn't look that good but it makes life very difficult for the opposition."
Disappointed Leicester boss Micky Adams joined Allardyce in his condemnation.
"It's a nonsense and a mockery," he said.
"Good old Sammy (Allardyce) has found a chink in the offside law. It's cost us... a point is no good to us."
