The proposals include the removal of fees for listed building consents, conservation area consents and demolition within areas of townscape or village character.
Certain concessionary and reduced fees would also be removed, fees for single dwellings would be simplified and a "more appropriate" fee for applications requiring an environmental assessment would be charged.
An increase in the maximum fee for housing developments, for the construction of industrial and commercial buildings and for plant, machinery and wind farms is also suggested.
The service has found that the downturn is continuing to have a significant impact, producing major fluctuations in fee income levels.
The number of applications has fallen 30 per cent from 27,906 in 2007-08 to 19,557 in 2009-10. Fee revenue is expected to raise £12.8 million in 2010-11, down nearly 40 per cent from 2007-08.
The second stage of the fee review will consider issues not covered in the consultation. These include fee anomalies, maximum fees and process costing.
The department is making savings through the redeployment of staff to jobs elsewhere in the public sector, ending casual employment and cutting overtime as well as carrying out a review of operating costs and corporate services. The consultation ends on 4 January.