Some nurseries say they are facing hikes of more than 100% in April following the national revaluation.
Linda Pirie, who owns three nurseries in Aberdeenshire, said her clients faced a 15% rise in fees.
The Scottish government said there was a relief package and it was up to local authorities to address local issues.
Mrs Pirie told BBC Scotland: "I think some people will go out of business.
"I think if we have to put up fees by what we need, we are going to lose clients."
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A Scottish government spokesman said: "The Scottish government had already acted to cut the poundage by 3.7%, take 8,000 businesses out of the Large Business Supplement and extend the Small Business Bonus scheme, an overall tax cut worth Â£155m next year, to help those who might be impacted by a revaluation."
He added: "From April, more than half of businesses will pay no rates and seven out of 10 will pay the same or less.
"The total updated rates relief package is now worth over Â£660m, including the additional support for key sectors of hospitality and renewables nationwide and those with offices in Aberdeen and Aberdeenshire, and councils are empowered to apply further reductions to address any local issues as they see fit.
"Any business that is concerned about its valuation should contact the assessor and discuss how they worked out the provisional value. Companies have until September to appeal and we would encourage firms to take up those opportunities."
Rateable values are changing for the first time since 2010 after a national revaluation by The Scottish Assessors' Association.
A nursery owner has warned that parents face having to pay the price of rising business rates rises and that some nurseries could go out of business.