New figures obtained by the Evening News show that 10,552 appeals were lodged against the bills that came into force in April by last month's appeals deadline. Assessors have admitted that half of the cases will not be resolved until 2012 at the earliest.
Many firms have said they have seen annual bills more than double as a result of the revaluation, which is carried out every five years. They say the rise, which is based on values in 2008 before the property market slump, is hitting them hard during the recession.
Business leaders today criticised the amount of time it would take to resolve appeals - saying that some firms will be put out of business long before they are heard.
Ron Hewitt, chief executive of the Edinburgh Chamber of Commerce, said: "The fact of the matter is it is a pretty clear vote that the rates reassessment has been an unjust action based on rateable values at the peak of the market.
"Many people are facing large rises - some of 100 per cent or more - and there is no way that rents have gone up that much."
He said that it "beggars belief" that half of all firms will not have had their appeals resolved less than 21 months after they were hit by the new rates bill, and added: "The businesses that are really suffering might not even survive that long and certainly jobs will be lost; jobs are already being lost."
Mr Hewitt is calling on the Scottish Government to intervene and alleviate the stress many businesses' finances are under as a result of the changes.
Assessors from the Lothian Valuation Joint Board judge the rateable value of a property every five years and a formula is used to set the business rates bill for each occupier.
The new valuations came into force in April this year and are judged on the state of the economy in early 2008.
The Evening News has revealed a string of organisations that have been hit with rises in rates, include pubs, shops, nurseries, hotels and NHS Lothian.
Joan Hewton, assessor with the valuation board, today said the first appeals hearings would take place in February, with 50 per cent expected to be resolved "during 2011".
The final date for resolution is the end of 2013.
Asked why the process will take so long, Ms Hewton said: "Most appeals are lodged by chartered surveyors who are specialised in the field of rating.
"Those surveyors are limited in number and many deal with appeals throughout Scotland and England - thus have limited resources to deal with appeals in the Lothians quicker.