Holyrood has made assurances by saying the move is just part of a plan to support town centres and that rates relief will still remain more generous than in England.
The new legislation is intended to encourage landlords to let properties.
But CBI Scotland said this would increase the burden on companies by £18m a year.
"This increase in taxation will make it more expensive for firms to invest and create jobs and is simply the wrong approach," said CBI Scotland director Iain McMillan.
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"For many firms this tax rise feels more like a stick than a carrot. After all, commercial premises are rarely left empty on purpose as they do not generate an income."
David Melhuish, director of the Scottish Property Federation, said: "This will lead to further administrations as landlords struggle to pay an 80% increase in their vacant rates costs and will put pressure on ratepayers who cannot sublet or dispose of unwanted property assets."
MSPs are due to vote today on the final stage of the Local Government Finance (Unoccupied Properties) (Scotland) Bill.
A Scottish Government spokeswoman said: "Scotland's town centres are blighted by empty buildings and our suggested reforms will encourage landlords to let out empty properties as well as create new rates discounts for entrepreneurs who take on these properties.
"Reform of empty property rates, which currently costs over £150 million a year, is only part of our proposals to support town centres.
"The total relief package offered by Scottish Government now exceeds £500 million per year and has either eliminated or substantially reduced business rates for three out of every five commercial properties."
(IT)
