The Federation of Small Businesses said three out of five survey respondents in Scotland did not know how their business rates bills were calculated, with many complaining the system is confusing and inaccessible.
"The majority of our members report that they find their rates calculations incomprehensible," said Colin Borland, head of external affairs in Scotland for the FSB. Mr Borland said businesses need to be given clear guidance on how their bills are calculated.
The survey reveals widespread concerns that the estimates of the rateable values of properties (used to calculate rates bills) may be inappropriate.
Bills are calculated by multiplying the rateable value of a property by a poundage rate set by the Scottish Government.
But respondents expressed frustration that very similar premises seem to be valued differently.
The FSB noted the last five-yearly revaluation of properties took place in 2010, and was based on data gathered before the economic downturn in 2008.
The body detailed its concerns in a submission to a consultation by the Scottish Government as part of a review of business rates. Responses to the consultation are due by Friday.
However, the FSB said the rates relief provided under the Scottish Government's Small Business Bonus Scheme has "mitigated the impact of other spiralling overheads for many recipients" since its introduction in 2008.
Separately, the Forum of Private Business (FPB) said 94% of respondents to a survey of around 100 UK firms, including about 10 from Scotland, said business rates are too high. Two-thirds of those also said they saw no real benefits for the amount of money they were spending on the tax.
The results reveal widespread concerns about the effect of changes made to the UK tax system.
"In total, 28% of business owners thought the fairness of the tax system had deteriorated, compared to 17% reporting an improvement," said the FPB. "One-quarter said it had become more complex, while 14% said it has simplified."
The FPB said 26% said the tax system had become less efficient, while 10% thought it had improved.