David Lonsdale, chief executive of the Scottish Retail Consortium, said the increase was not justified by the promised improved performance by council planners:
He said: "Retailers want to see an effective and well-resourced planning system … However, it is far from clear that this further above-inflation rise in fees, coming on top of last year's bumper 20% increase, has been accompanied by a commensurate and demonstrable improvement in service to retail and other commercial applicants.
"We also want to see the Scottish Government's business rates incentivisation scheme rejuvenated, to encourage a more business-friendly approach towards local development, with the revenues transparently re-invested in supporting the local economy."
November's planned 5% rise follows a 20% increase in April 2013.
But Craig McLaren, Scotland and Ireland director of professional body the Royal Town Planning Institute, said: "We need to work towards ensuring that fees cover the cost of processing planning applications and that this income is directly re-invested in the planning department."
Work commissioned by Heads of Planning Scotland from the Chartered Institute of Public Finance and Accountancy showed that the average fee income covers only 73.8% of the costs of processing planning applications from receipt to appeal or local review.
A recent Scottish Government planning circular said of the fees: "The Scottish Government considers that the proposed 5% increase will strengthen resources and the capability of the planning authorities to deliver a high performing planning service."