Scotland's FA is likely to alter its constitution next month to dock points or relegate clubs for racist or sectarian chants by their fans.
SFA president John McBeth was speaking to BBC Sport amid claims that Uefa could appeal its own decision to find Rangers fans not guilty in Villarreal.
World football's governing body wants new measures to tackle the problem.
And McBeth said: "If we want to stay in Fifa, we must comply with what they want and will discuss it at our agm."
Under Fifa Circular No.1026, which takes effect immediately, world football's governing body wants clubs to be:
The circular adds that a national association will have its team banned from international competition for two years if it does not comply.
McBeth said there was a "very real possibility" that points could be deducted from Scottish clubs next season if they fall foul of the new regulations.
"I cannot foresee the SFA challenging this," he said.
"It will also mean that the SFA will have to monitor games more closely."
McBeth had revealed earlier this week that, working along with the Scottish Executive, the SFA would be introducing banning orders to stop fans found guilty of discriminatory chants from re-entering football grounds.
However, the SFA is concerned about the practical problems of how to police the new regulations demanded by Fifa.
McLeish warns Fifa over chants
It also fears that the clubs themselves could challenge, through the legal system, any punishments imposed by the SFA.
While racism has not been a major issue in Scotland, sectarianism has been a long-standing problem, especially for Glasgow rivals Rangers and Celtic.
European governing body Uefa investigated alleged discriminatory chanting by Rangers fans during the two legs of the Glasgow club's Champions League tie with Villarreal.
They found Rangers not guilty but appeared to suggest that it did this because it viewed sectarianism as a specific Scottish issue in which it did not wish to become involved.
Head of communications William Gaillard told BBC Sport described Uefa's decision as "a statement of humility".
However, reports have since suggested that Uefa officials who carried out the investigation want to appeal the decision and have until the middle of next week to lodge any challenge.
It is being claimed that the report had recommended a £25,000 fine and the closure of a stand at Ibrox Stadium.