Recorded by the London Philharmonic Orchestra at the famed Abbey Road Studios in a six-day marathon more than a year ago, the anthem played after Szilagyi's success on Sunday was considered out of sync with its traditionally slow and melodic pacing.
"We asked the organisers to change the Hungarian anthem for any future gold medals and (London organisers) LOCOG said yes. We thank them for that," Hungarian Olympic Committee press contact Oliver Torok said by phone.
"The rhythm and tones were off," said Jeno Kamuti, chief of the Hungarian fencing team and two-time silver medalist in men's foil.
Hungary's biggest sports daily, Nemzeti Sport, called Sunday's rendition "weird".
"The anthem isn't the same in London. Listening to the anthem is the most solemn moment after a gold medal. But this time, after Aron Szilagyi's gold, something seems to have been wrong. Several tracts of our national song were weird."
No formal protest was made to organisers after Sunday's gaffe, nor was any mention made of the incident at the after-match news conference, which ended late.
"It was late and so we decided to take this up in the morning," the Hungarian Olympic Committee's Torok said.
The recording was one of 205 anthems conducted by Philip Sheppard and commissioned as a gift to the International Olympic Committee, a spokesman for the London organisers said.
It was not the first problem with protocol at the Games.
On July 25, the North Korea women's soccer team walked off after the South Korea flag was mistakenly displayed before their match against Colombia, delaying it for an hour.