The Scottish Parliament's Economy, Energy and Tourism Committee said the rise would help local planning authorities struggling to keep up with the number of onshore wind applications being made by investing in more staff and resources to deal with the influx.
However, the Committee also recommends that planning authorities be required to become more efficient in return for higher fees.
"The Committee is supportive of fee increases for larger-scale planning applications where these will not disadvantage community developers," says the Committee's report of its inquiry into Scotland's ability to hit its target of generating 100% of its electricity from renewables by 2020.
"The Committee recommends that the Scottish Government considers whether, in return for higher fees, planning authorities could address duplication of effort for developers and improve efficiency, for example by taking on tasks such as gathering information on cumulative visual impact from their own records, rather than each developer having to undertake this task separately."
The fee rise recommendation follows the Scottish Government's unveiling of a £300,000 fund in September to support planning authorities processing wind applications. In its report, the Committee rejected calls by some planning authorities to impose a moratorium on wind farm planning applications until the current backlog was dealt with.
Overall, the Committee's report was confident Scotland could hit its 2020 target of 100% renewables, notwithstanding the challenges within the planning system and the ability of developers to gain access to project finance.
The Committee also used the report to criticise the UK government for "breeding uncertainty" by allowing a further review of Renewable Obligation Certificates (ROCs) in 2014 after agreeing revised rates in July.