Jose-Marcia Garcia-Aranda accepted that some in-game calls were "not fully correct," but that mistakes were inevitable.
"Some of them are not good decisions on the field of play and this for human beings, is natural," he told reporters Monday. "We are trying to improve those decisions that we consider are not good enough and for that reason we are training every day."
Garcia-Aranda said World Cup referees should not have to explain their most controversial decisions to players and media a stance backed by some of the 30 elite officials working at the tournament in South Africa.
"We are not ready for that," said Switzerland's Massimo Busacca, who is recognized as a clear communicator and candidate to officiate the final. "They will complain too much."
Uruguayan Jorge Larrionda said fans in South America did not like seeing referees talk about themselves.
"Maybe it is better to close the mouth," said Larrionda, who will work his third match of the tournament when Australia plays Serbia on Wednesday.
Most of the 30 spoke Monday in an open practice session at a school near Pretoria, though Mali's Koman Couilbaly and Stephane Lannoy of France were absent after working match duties on Sunday.
Lannoy was criticized for failing to spot a handball before Brazil's second goal in its 3-1 win over Ivory Coast, and sending off Kaka by showing a second yellow card when opponent Kader Keita appeared to run into the Brazilian playmaker.
Couilbaly drew worldwide attention by disallowing a goal that would have given the United States a late lead against Slovenia last Friday, and infuriated American players by not explaining his judgment.
He earlier showed a yellow card when the ball struck Robbie Findley in the face, meaning the U.S. forward is suspended for the final group match against Algeria on Wednesday. That punishment was "completely wrong and unfair," Findley's teammate Landon Donovan said.
Garcia-Aranda said FIFA would not discuss individual decisions by its referees, which were supplied by each of the six continental football bodies.
"FIFA is proud of having good referees from all the confederations," the Spanish official said. "The level of all these referees is very, very high."
Mistakes were being exposed by the scrutiny directed at World Cup matches, Garcia-Aranda said.
"We have (seen) excellent decisions on the field of play," he said. "Later, maybe with 32 cameras, thousands of people assessing this kind of situation, we realize these decisions were not fully correct."
FIFA has prepared the 30 referees and their two regular assistants with physical and psychological training programs, and will pay each referee a fee of $50,000 (euro40,000) for the tournament.
Garcia-Aranda said referees had a duty "to try to implement the laws of the game but not to explain every single situation," otherwise they won't be focused entirely on the game.
"Nobody can say the credibility of football is, let's say, in doubt."