Edwin Atkinson, director general of the association, said: "There have been one or two reports of small importers of small volume brands having to give up importing them.
"We alerted the Chancellor to our concerns from the start and said small importers might be disadvantaged. Now there's evidence this has been the case."
While large drinks companies have shouldered costs, companies with niche or specialist brands have struggled to meet the one-off capital costs associated with preparing their businesses to fix stamps to bottles of spirits, Atkinson said.
Independent retailer David Simmonds, of Derby's Red Zebra, said: "We've noticed that some of our small suppliers have been affected. We can't get hold of certain brands because they just couldn't afford to subscribe to the scheme."
Most independent retailers have had an easy transition to the scheme, Atkinson said. "So far we've not had any bad reports.
"There's still some old stock around, such as slow-moving super-premium brands, but retailers don't need to panic. It's quite legal as long as you can show invoices and show duty has been paid."