Firms currently get a 50% discount on business rates for vacant premises. How-ever, Holyrood has approved changes to make them pay 90% of the charge.
Chief executive Liz Cameron accused the SNP of "demonstrating, at best, a total lack of understanding of the pressures facing businesses in Scotland".
She said it would not rejuvenate Scotland's high streets or reduce the blight of empty properties, adding that a similar measure in England four years ago had no positive impact.
Housing Minister Margaret Burgess said: "While people across Scotland need new homes, it is completely unacceptable that 25,000 houses are lying empty."