Two-thirds of clean share classes are more expensive than their bundled equivalents, according to research by consultancy firm Adviser Asset.
The firm has written to the Financial Services Authority (FSA) to warn that the practice of providing a single clean fee to all platforms is "anti-competitive".
Of the 1,317 clean share class funds analysed 66.4 % could be obtained at a lower cost via another class of the same fund after the application of rebates.
Only 21.6% could be obtained at a lower cost with the clean share class.
Earlier this month, IFAonline found a number of providers had raised charges on their funds when moving to clean share classes, either through premium pricing or increased administration fees.
The average difference in charges between clean share class funds and lower cost versions of the same fund is 25bps in favour of the rebated funds, according to Adviser Asset director Colin Turton.
In the letter, Turton said the clean share class "has the benefit of increased transparency, but brings with it some significant price competition implications".
The proposed outlawing of cash rebates presented an additional problem, he said.
"Almost all players that we have spoken to in the advised platform market are against the introduction of a ban on cash rebates to consumers.
"We would therefore strongly urge you to reconsider the proposals in light of the new data we have provided.
"The provision of cash rebates currently provides platforms and fund providers with a simple and highly flexible way of implementing the results of fund charge negotiations.
"The ease and frequency with which differential charging for funds can be implemented by fund providers and platforms is a key driver and enabler of effective price competition."
If the FSA does indeed ban cash rebates, it could either continue with its policy of enforcing a single clean fee, or force fund providers to make clean share classes for each individual platform.
However, Turton argued the most practical way to meet the objectives set out in the FSA's platform paper - greater price competition and reduced fund charges - is for fund providers have one share class, but with the facility to offer different levels of unit rebate to the each platform.
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