Dr. Richard Johnston says he wrote to Health Minister Stephen Mandel a few weeks ago saying the association strongly supports banning menthol.
He says studies show youth menthol smokers smoke more cigarettes than their non-menthol smoking peers and they are three times less likely to quit smoking than non-menthol smokers.
Johnston praised the government for other steps it announced last Thursday to protect young people from tobacco.
They include making it illegal to smoke in a vehicle when there are children inside.
Johnston says Mandel has indicated the province will take another look at a menthol ban sometime in the future, and when it does he says the association will advocate for the change.
"It is disappointing, therefore, that menthol is not on the list of banned substances at present," Johnston wrote in a letter to Alberta physicians Tuesday.
"There is still opportunity to advance a menthol ban. The AMA will advocate accordingly as will the Canadian Cancer Society, Action on Smoking on Health and many others."
The federal, Ontario and Manitoba governments have also balked at including menthol in flavoured tobacco ban legislation.