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The Manx Treasury has confirmed that some rates demands for 2012 to 2012 were sent to charities without the reductions allowed for their charitable status.
It says it has apologised for any confusion and inconvenience caused by the error.
A media release says officers in the Treasury are committed to achieving high standards of accuracy, and an investigation is under way into how the mistake was made.
The Treasury says it will be contacting all the affected charities directly, and the erroneous rating demands will be cancelled and reissued following the correct procedures.
Any overpayments made by charities will be refunded to them.
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