The statement said that the increase would generate between £4 million to £5 million to support the work of planning authorities and would see Scottish planning fees remain lower than those in England and Wales for most categories of development.
A Scottish government consultation document published in March had proposed fee increases for residential, retail and energy generating developments. The consultation had proposed to set the maximum fee at £100,000 - up from a current cap of £15,950.
Homes for Scotland chief executive Philip Hogg said that the minister had "set fees at a far lower level than envisaged in his consultation". Hogg said that the fees "will not negatively impact the industry’s ability to promote new projects".
Mackay’s statement also said that a "high level group" would review planning performance and look at proposals to link performance with wider reform of planning fees.
The statement added that the Scottish government will pursue a statutory mechanism to "penalise authorities who underperform in the longer term".
Mackay confirmed £673,000 of one-off funding to help local planning authorities deal with wind farm applications.
The minister also announced £55,000 of additional funding for Planning Aid for Scotland to increase young people’s involvement in planning and to deliver pilot projects to investigate alternative ways of delivering charrettes, design workshops through which local people are helped by experts to draw up development plans for their communities.
In addition, Mackay said that the Scottish government would provide an additional £20,000 to Heads of Planning Scotland for training support.
Mackay said: "Following discussions with stakeholders and further meetings a commitment around further performance has been reached, in that context new resources through planning fees will help planning authorities deliver.
"The increase is designed to allow authorities to improve performance, while keeping overall planning fees in Scotland lower than the English equivalent.
"We know that some planning authorities are experiencing particularly high volumes of applications for wind turbines, and the extra funding being announced today will help by supporting assessment, bringing in expertise, or more staff, to deal with the applications."