However, it's unclear as to how long it could take the Ministry of Health to revoke the stores' licences.
"No thought was given to the effects on our community when the government was drafting this legislation," said Ms O'Leary.
Mayor Julie Hardaker said the council has made the best of a bad situation. "We've given the Ministry [of Health] guidelines for when they issue licenses.
"I think it is a good policy, but it is making the best of a bad situation. It is out of our hands now."
Councillors expressed their concern over public expectation as to what would happen once the policy was passed.
"The expectation may well be that the Hamilton City Council will close down the Hamilton East puff shop," Councillor Ewan Wilson said.
"I'd like to thank our friends in central government; I have never seen such appallingly drafted legislation. Who would draft legislation and forget to put regulatory frame work in place?"
The Psychoactive Substances Regulation Authority will make the decision on whether or not the policy is implemented.
"If we're going to sell this drug it's better to be sold where people can see the [effect] of it. We have to remind the public that the Hamilton East shop will not be closing on Wednesday.
"But the wonderful news is they do get to vote in October when it comes to central government options," Mr Wilson said.