President Sepp Blatter, who had already publicly criticised the standard of the assistant referees, now wants to review the way every official is chosen and assessed.
One or two major mistakes have been made
Fifa spokesman Keith Cooper
And he personally stepped in to oversee which officials were appointed for the semi-final matches, in an effort to avoid any further blunders.
Tournament organisers have conceded that controversial decisions have affected crucial games.
"One or two major mistakes have been made which is a concern," said Fifa spokesman Keith Cooper.
"Referees are only human and errors can never be entirely eliminated."
Spain felt they had two good goals disallowed against South Korea
The standard of refereeing was generally applauded after the group stages, but has come under fire during the knockout phase.
Italy and Spain were both extremely unhappy at going out to what they saw as poor decisions.
Both teams lost to co-host South Korea - Italy to a golden goal and Spain on penalties.
But Italy had their fifth goal in three games disallowed and Francesco Totti harshly dismissed during their second-round defeat.
Official Spanish protest
And Spain had two goals disallowed that replays suggested should have stood.
Spanish football federation president Angel Maria Villar has resigned from Fifa's referees commission - and intends to make a formal protest.
"We will explain that we have been negatively affected by their decisions," he said.
"The damage has now been done, but we want to make sure that this sort of thing does not happen again."
Fifa spokesman Cooper meanwhile quickly dismissed talk of referees deliberately favouring co-host South Korea.
"Conspiracy theories crop up on all occasions and in 99% of the cases, they prove to be unfounded.
"This is one of those 99% of occasions."
And he reaffirmed that idea of video replays to help the officials was "not on the agenda".
I believe referees will be fair to us and make fair decisions
Germany goalkeeper Oliver Kahn
Scottish referee Hugh Dallas added: "There is no question that anyone from Fifa has spoken to the referees and told them to look after Korea and Japan.
"If that was the case you'd have to ask why haven't Japan also gone through?"
South Korea play Germany in their semi-final encounter on Tuesday.
But Germany goalkeeper Oliver Kahn said he is not concerned by the prospect of poor refereeing decisions.
"I believe referees will be fair to us and make fair decisions," said the German captain.
"Even if we did face an unjust call, we won't dwell on them for too long during the match."
"Spain were too obsessed by what they perceived by as wrong decisions by the referee.
"Italy too allowed it to get to them. In the end it just worked against them."