Hong Kong's football governing body expressed "disappointment" Wednesday that FIFA is investigating the booing of the Chinese national anthem at a World Cup qualifier between the city and its mainland rivals.

Hong Kong fans jeered and turned their backs during the "March of the Volunteers" anthem, which the semi-autonomous territory shares with China.

They also held up white signs saying "boo" in English during last Tuesday's sold-out match at Mong Kok Stadium, attended by around 6,000 fans.

The investigation follows warnings against audible booing from world body FIFA, which fined the Hong Kong Football Association after fans jeered their own anthem at previous qualifiers.

"The HKFA is disappointed, but not surprised, to learn from FIFA that disciplinary proceedings are being opened in respect of booing at the recent Hong Kong versus China football match," its chief executive officer Mark Sutcliffe told AFP Wednesday.

"The HKFA will be submitting a response to FIFA stating that the booing was carried out by a small section of the crowd and pointing out the mitigating actions taken by the HKFA prior to the match to... avoid this situation," Sutcliffe said.

Fans from both teams were strictly segregated, using separate entrances and even different toilets, in a bid to head off any potential trouble in a district that was one of the centres of the 2014 pro-democracy protests.

The joint 2018 World Cup and 2019 Asian Cup qualifier follows last year's "Umbrella Movement" pro-democracy protests, which gripped the city and underlined discontent with Beijing's rule.

The match, which ended in a goalless draw, left China's hopes of reaching the 2018 World Cup in Russia hanging by a thread.

The perennially underachieving national team stands third in its group, with two games left, and is struggling to reach the next round of Asian qualifiers.