Over 40% of companies are facing an increase in their business rates after the revaluation earlier this year, according to a survey by the Northern Ireland Chamber of Commerce.
And nearly a quarter of those affected say that the rising rates bill has had a "significant" impact on their business by eating into their bottom line.
Firms told the Chamber's quarterly economic survey, which is produced with accountants BDO, that their prices were no longer as competitive and that they were having to cut costs in areas such as overtime and training.
And the majority of respondents told the survey that they felt rates should be reformed "to reflect economic reality" - with many believing that rates should reflect business size rather than property size.
Chamber chief executive Ann McGregor said: "Business rates is a tax that hits companies of all sizes long before they make a profit, and impacts on business growth and investment.
"Northern Ireland Chamber members are of the view that the business rates system in Northern Ireland is in need of reform to make it more reflective of economic conditions."
The revaluation earlier this year revised the rateable value of properties in light of the property crash.
But it also resulted in many businesses in areas like the Cathedral Quarter, which have only taken off in the last 10 years, experiencing a massive increase in their bills.
Ms McGregor said the Chamber was engaging with the Department of Finance and Personnel to encourage the Finance Minister to hold a "fundamental review" of rates.
"We believe that the review provides the perfect opportunity for a root and branch reform of business rates in Northern Ireland which at the very least finds some way to spread the costs more evenly and lessen the burden on existing ratepayers.
"Companies also need a much clearer understanding of what their business rates actually pay for."
Despite the concern over rates, the survey presented a positive showing in most areas though manufacturers were mixed in their take. Their domestic orders had improved and more manufacturers in Northern Ireland were planning to take on new staff.
But overseas, the picture was less cheerful, with more businesses reporting a fall in export orders than an increase.
Businesses in the services sector - a classification encompassing everything from estate agents to restaurants - were also positive in many indicators, except exports. But services firms in Northern Ireland were the lowest in confidence of any region in the UK.
Exchange rates and competition were both major concerns.
BDO partner Brian Murphy said the results were "encouraging, confirming continued improvement across the economy".
Number of businesses facing a hike in rates after 2015 revaluation