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 by allowing them to invest in more staff and resources to deal with the influx.
"The committee is supportive of fee increases for larger-scale permitting applications where these will not disadvantage community developers", the committee said in a report published last month on its inquiry into Scotland's ability to hit its target of generating 100% of its electricity from renewables by 2020.
In return for the increased fee income, councils should become more efficient, the committee recommended. For example, they could gather information on cumulative visual impact from their own records, rather than each developer having to undertake this separately, it suggests.
The fee rise recommendation follows the Scottish Government's unveiling of a £300,000 fund in September to support councils processing wind applications. In its report, the committee rejected calls by some councils to impose a moratorium on wind farm permitting 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 permitting system and the ability of developers to gain access to project finance.
The committee also used the report to criticise the Westminster government for "breeding uncertainty" by allowing a further review of Renewable Obligation Certificates (ROCs) in 2014 after agreeing revised rates in July.
The report attacked those who have claimed that wind would damage Scotland's tourism industry. No witness provided robust evidence that this was the case, the committee said.
US entrepreneur Donald Trump ran a venomous anti-wind power campaign in his bid to block Swedish utility Vattenfall's 100MW European Offshore Wind Centre from being built near to Trump's planned £750 million luxury hotel and golf course in Aberdeen Bay on the east coast of Scotland.
Sam Gardner, senior policy officer at environmental charity WWF Scotland said: "Trump really needs to get the message that he is massively out of line with public opinion in Scotland."