Riverhill Coffee Bar in Glasgow's Gordon Street is selling the cupcakes, made on site at the city centre cafe, for £2.
The treats - marketed as 'Breaking Bad Crystal Meth cupcakes' - include the distinctive blue topping which looks like the crystal meth manufactured by Bryan Cranston's character in Breaking Bad.
The character, Walter White, is a chemistry teacher who takes to 'cooking' and selling the drug to pay for his treatment for terminal cancer.
He goes from a mild mannered father to a ruthless criminal mastermind known as 'Heisenberg' over the course of the series.
Christine Duncan, chief executive of Scottish Families Affected by Alcohol and Drugs, said: "The glamorising of drugs is completely distasteful.
"We know from our membership base that the impact of drug misuse on families includes financial instability, breakdown in family relationships and the loss of employment."
The Green Party's city centre councillor, Nina Baker, said: "The cafe might try to pass it off as a joke, but I don't think it's funny.
"It doesn't sit well with the work that is being done to tackle drug abuse. Quite frankly, there's nothing funny about recreational drug use."
Glasgow man James Lees, 29, is the brains behind successful food blog James vs Burger.
He watches Breaking Bad and said the cupcakes should be taken as nothing more than an in-joke among fans of the show.
He said: "The only people who would even get the reference are fans of show.
"It's clearly a bit of fun that has come about because the show is just weeks away from its grand finale.
"The show itself is about one man's descent into madness, it certainly doesn't glamorise drugs and neither does someone selling a cupcake with blue sprinkles on top."
A spokesman for Riverhill Coffee Bar said: "We absolutely do not condone the use of drugs. Breaking Bad is such a huge, cult hit and this was simply us jumping on that bandwagon and making something that would appeal to fans of the show."