John Orysik, spokesman for Coastal Jazz & Blues Society, said that the society regrets the inclusion of dispensaries advertising in their program guides.
"It's the first time something like this has happened in 30 years." he said.
Orysik also said that the ads were pulled from all the digital and online copies of the festival program, but the initial run of program flyers is still in circulation.
"Marijuana advertising is illegal," said Sean Upton, media relations officer with Health Canada, in an e-mail statement.
The statement said that Canada's Food and Drugs Act and Narcotic Control Regulations prohibit the advertising of marijuana.
Under the Food and Drugs Act, offenders could face a maximum penalty of 5 million dollars, 2 years in prison, or both.
Orysik says that Coastal Jazz outsources its advertising sales to a private firm, and that mechanisms have now been put in place to ensure that all advertising is signed off and checked for legality.
"We're complying with the measures that have been outlined," said Orysik.
"We're on to putting on a jazz festival now. This is what we're focused on."
The Supreme Court of Canada ruled last week that medical marijuana is now legal in all forms.
The City of Vancouver is currently considering regulating medical marijuana dispensaries.