The claims were made after the Lands Valuation Court in Edinburgh ruled against firms that said rates on their buildings were too high because they were set before the credit crunch.
The appeal by the Mercat Shopping Centre in Kirkcaldy, Fife, and the Overgate Shopping Centre in Dundee has set a precedent for more cases in Glasgow, Edinburgh and across Scotland.
Other high street names involved in rates appeals include Santander and Superdrug.
It is understood that, had the shopping centres won the case, it would have meant a reduction in rates of up to 30%.
Rates are property-based taxes and the companies claim they were set at a time when there was a different financial landscape and are therefore unfair.
Current business rates were calculated in 2008, before the extent of the downturn became apparent.
But the court ruled that the ongoing economic decline is not a suitable reason for rateable values to be reduced.
However, the Scottish Government, which is responsible for setting up the controversial policy for business rates, plans to hold a consultation on the system after widespread concerns.
The Federation of Small Businesses (FSB) in Scotland, Scottish Retail Consortium and Scottish Chambers of Commerce were among those who said the decision was disappointing.
Stuart Mackinnon of the FSB Scotland said some may be unable to sustain levels of rates.
He added: "There are a lot of businesses whose margins are extremely tight and an inflexible system will affect them. Some will make the decision to relocate on the basis of costs.
"Firms with have high operating costs because of business rates have to pass that cost to their customers."
Garry Clark, head of policy and public affairs at Scottish Chambers of Commerce, said: "This decision by the Lands Valuation Appeal Court is disappointing and flies in the face of common sense.
"It leaves tens of thousands of businesses struggling under the burden of a rates bill based on pre-recession rental values."
A spokesman for the Scottish Retail Consortium said it was "crucial that each of the five-yearly revaluations delivers an accurate assessment of rateable value at that time and a distribution that leaves everyone paying a fair share".
Peter Muir, director and head of rating for Colliers International in Scotland, which has been involved in the Glasgow appeals, said: "The appeal outcome is a severe disappointment to ratepayers throughout the country.
"Non-domestic rates is a significant outlay to any business and this decision means that, in areas where rents have fallen since April 2008, rateable values must stay at their current levels.
"I would call upon the Scottish Government to urgently review the legislation with a view to amendments being made to allow ratepayers to reduce their annual liability to reflect downturn of rents."
Gordon Martin, of property managers GVA, said: "Essentially this means ratepayers across Scotland continue to pay rates well out of line with prevailing levels of value.
"This decision is a real body blow to struggling businesses and may limit the ability of ratepayers to challenge their assessments. Retail, industrial and office occupiers continue to pay rates based on levels that bear no relation to today's levels of value and create an unfair burden on business."
A Scottish Government spokesman said a review would be carried out. He added: "The outcome of the Court of Session's Mercat rating appeal found in favour of the assessors and agreed they had correctly applied the legislation.
"This Government is focused on retaining Scotland's reputation as the most supportive environment for business in the UK and the total rates-relief package offered exceeds £500 million a year.
"We have also committed to review the business rates system this year to ensure rates reflects the current economic challenges and opportunities."
