Fans in the southern Chinese city had also booed the “March of the Volunteers” — the anthem which they share with China — during two other home games earlier this year, prompting a warning from the world governing body about future conduct.
Last year’s “Umbrella Movement” mass pro-democracy protests have soured attitudes in the semi-autonomous territory towards the Chinese authorities in Beijing.
But the HKFA sought to play down a chorus of boos from sections of the crowd at Tuesday’s match at Mongkok Stadium, which Qatar won 3-2.
“In my opinion, the number of people booing the anthem and the noise created by them was less than at the other two home matches,” HKFA chief executive officer Mark Sutcliffe told AFP.
“They and the anthem itself were drowned out by people singing their support for the Hong Kong team,” Sutcliffe added.
Possible FIFA sanctions could include having to play the next home qualifier, which would be against China in November, behind closed doors.
“I would be disappointed if FIFA placed any further sanctions on the HKFA,” Sutcliffe said.
“We will just have to wait and see,” he said, adding that the HKFA had taken steps to encourage people to respect the anthem.
Sutcliffe had on Monday appealed to fans to not “use the match as a means of making a political statement”.
“The eyes of the world and FIFA in particular will be watching to see that fair play prevails,” he said in a letter on the HKFA website.
Fans went wild as Hong Kong scored two late goals after trailing 3-0 in Tuesday’s match, but were unable to find the equaliser.
The team’s next qualifier is away to Bhutan in October before the rematch with China in November. The two sides played out a 0-0 draw in Shenzhen just across the border from Hong Kong, last week.
The second round of Asian qualifying for Russia 2018, which finishes in March, features 39 teams and also doubles up as qualifying for the 2019 Asian Cup in the United Arab Emirates.