Draft guidance from HM Revenue and Customs states that if the rebate agreement is between the adviser and the client, then the adviser is responsible for deducting the tax and the reporting.
Many advisers may not be aware of this and believe this task is up to the platform or the provider.
Neil MacGillivray, head of the technical support unit, at James Hay, said: "Advisers could find themselves responsible for the deducting of tax and reporting of this if they hold the agreement with the client on the rebating of commission. This agreement is typically between the investor and the fund platform, although it can be as a result of an agreement between the investor and their adviser."
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He said the potential outcome would be more providers moving to clean funds for all wrappers. However, he said HMRC accepted it would be difficult for advisers to make the changes within two weeks.
He said: "Systems will need to be amended to allow the deduction of basic rate income tax from payments but they have accepted that this may not be possible with a two week deadline.
"Rather than delaying implementation, HMRC has agreed to accept an approximation of the tax deducted at source up to the calendar year 2013 providing that this is accurate as reasonably possible and that payer makes arrangement to update their systems by the end of 2013."

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