The League One leaders could face court action because their crest breaks ancient heraldic law.
Their current crest consists of a scroll bearing the club's name, underneath a saltire and therefore falls foul of Scots Law and is anregistered Coat of Arms.
It follows a complaint from a member of the public, believed to be a fan of a rival club.
Ayr United are the second Scottish club to be affected by the ancient Court of Lord Lyon this year, as fellow League One side Airdrieonians had to scrap their badge for a similar reason.
Ayr United must now apply to the to redraw their badge, while they also face a fight to retain the saltire on their crest.
The option to register their current design is understood to be a non-starter due to the presence of the saltire.
The right to display the flag is usually restricted to national institutions, and has been an integral part of the club's crest since 1957.