A code of conduct for spectators laid down by the Organising Committee outlaws flags other than those of Olympic members.
And although the UK is a member country, Scotland is not a member in its own right.
Now SNP MSP Jamie Hepburn is writing to the International Olympic Committee and the British Olympic Association, urging them to challenge the rule – which would also ban English, Welsh and Northern Irish fans from waving their country's national flags.
In addition it would prevent the Tibetan flag from being displayed at events.
Mr Hepburn said: "Athletes from across Scotland and the rest of the UK will be taking part in the Beijing Olympics, and fans should be allowed to show their support by waving the national flag of their choice.
"With participants like Andy Murray often wearing Saltires on their kit as a symbol of national pride it will be a shame if fans are not able to echo that by waving Saltires from the stands.
"I will be writing to the British Olympic Association and the International Olympic Committee and urging them to challenge this ruling."
Mr Hepburn also wants the situation for sportsmen and women competing in the Games to be clarified.
The Central Scotland MSP said: "On previous occasions Scottish athletes have been prevented from sporting a Saltire – it would be unfortunate where any athlete to find themselves in that position again."
He went on: "The Olympics should be a global celebration of different cultures and nationalities with this meeting in Beijing offering an opportunity for dialogue over the future of Tibet.
"China's crackdown on any show of support for Tibet – including the flying of flags – is out of keeping with the Olympic spirit and will raise many ongoing concerns as to China's commitment to improve free speech and expression in the run up to the Games.
"That it will have this unfortunate side effect for anyone wanting to fly a Saltire or the English, Welsh or Northern Irish flag may focus people's minds on the need for further dialogue between China and Tibet."
The Organising Committee guidelines states that spectators should not bring the following to any events: "Flags of non-members of the Olympics or Paralympics; flags or banners larger than 2m x 1m; flagpoles; any banners, slogans, fliers, brochures or samples."