Hong Kong Football Association (HKFA) vice-chairman Pui Kwan-kay told Young Post on Friday that Fifa's HK$77,000 fine was a reasonable punishment because it was not the first time local fans had booed the national anthem.
Fans at the home game against China at Mong Kok Stadium on November 17 held up signs reading "boo" during the singing of the national anthem.
Pui pleaded with fans not to repeat the booing in upcoming matches.
"This time Hong Kong was not stripped of points, and future matches won't be played behind closed doors, because the fans didn't cause the match to be stopped, or make trouble after it ended," he said.
"But a World Cup qualifier is not a platform for locals to express their discontent with the government or political issues. It is a good time to support the Hong Kong team so I hope the fans will be self-disciplined, and not boo the national anthem again."
Pui said any more trouble could lead to Hong Kong's disqualification from World Cup qualifiers.
Hong Kong was fined 5,000 Swiss francs (HK$39,000) by Fifa on October 6 after fans booed the anthem and threw a paper cup onto the pitch in another World Cup qualifying match against Qatar last September.