The 5% rise due to come into effect on November 1 follows a 20% increase introduced by the Scottish Government last year.
Groups representing Scotland’s tourism, retail, house-building and quarrying industries have attacked the increase as more than twice the rate of inflation.
They are calling for significant improvements to the service and speed provided by council planning departments.
Blair Melville, head of planning strategy at Homes for Scotland, said its members would be happy to pay higher fees in return for a quality service.
“However, the Scottish Government’s own planning performance framework monitoring shows a system which falls far short of the standards of customer service, speed and efficiency that the country needs if new development is to stimulate economic growth,” he said.
“There are some bright spots and good authorities, but too many are still offering inadequate service, and the worst-performing councils are undoubtedly acting as a drag on development.
“In addition, when public service spending cuts are continuing, we have no confidence that increased planning application fees will be used to improve staffing or service levels in planning departments.”
David Lonsdale, director of the Scottish Retail Consortium, said: “It is far from clear that this further above-inflation rise in fees, coming on top of last year’s hefty 20% increase, has been accompanied by a commensurate and demonstrable improvement in service to retail applicants.”
Marc Crothall, chief executive of the Scottish Tourism Alliance, said the industry was “yet to be convinced” of the need for the rise.
He said: “Managing costs remains a challenge and commitments to tourism investment need surety that the upfront costs are justified.
“Tourism firms will expect to see improvement in the service provided and especially in the pace of processing applications.”
Concerns have also been expressed by the Scotland-based British Aggregates Association, which represents independent quarry operators.
Secretary Richard Bird said the move would “exacerbate” the lack of experienced planners dealing with mineral planning applications.