Justice secretary Kenny MacAskill presented his case to MSPs earlier today who voted to implement the proposed system despite critics saying it could lead to a doubling of licensing fees in some areas.
MacAskill put forward the regulations to address the shortfall between the amount of money local authorities recover from fees and what it costs to administer the licensing system. Under the current system, only 63 per cent of costs are covered by income from fees.
The changes will be introduced under the new Licensing Act, which comes into force on Sep 1 2009.
Speaking before addressing the Justice Committee MacAskill said the fees proposed were "fair and reasonable to both the trade and to local authorities".
"Those who profit from alcohol have a responsibility to help pay for the costs," he said.
Although fees will be capped depending on the rateable value of the premises, the Scottish Grocers' Federation said many retailers would face a "staggering increase" under the new system.
SGF chief executive John Drummond said: "We believe local authorities will take advantages of the perimeters that Kenny MacAskill has given them. We hope they will be responsible and carry out what they need to carry out, but fear they will take advantage of the situation."