The rule change could have a big impact on consumers, as VAT rates on some goods and services vary substantially across the EU. For instance, the rate on ebooks in Luxembourg is 3 percent, while in the U.K. it is 20 percent.
While the rules could help some governments raise more tax revenue, consumers could feel the bite as companies raise prices to offset higher rates.
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In a KPMG survey of 156 businesses last September, 75 percent said they would consider increasing their prices from 2015 as a result of the changes.
"The additional costs of compliance, together with the increase in VAT, if fully passed on to customers, would result in an increase in prices of up to 11 percent," Amanda Tickel, partner at KPMG, said in the report.
She added: "With 53 percent saying their prices will only rise by 2-3 percent, this indicates that the majority of suppliers will be partially absorbing the costs."
The taxes paid—or not paid—by large companies has become a sensitive issue in the EU. Multinationals such as Starbucks and Amazon have come under fire for their alleged avoidance tactics.
Towards the end of 2014, allegations appeared in the international media that major companies had used rulings in Luxembourg to avoid paying tax.
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Nearly two-thirds of small businesses surveyed by KPMG did not know about the upcoming changes.