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The complaints follow the implementation of regulations that prevent pharmacists from adding a markup to medicines, and to charge only a fixed dispensing fee.
Many pharmacists have begun charging for a range of other services.
Council president Prof Peter Eagles said in a statement on Tuesday his organisation was aware of the concerns and uncertainty in the wake of the regulations.
Some pharmacists had voiced concern over the council's delay in finalising a revision of the rules on services for which a pharmacist could levy a fee.
At the same time consumers had reported cases of so-called administration fees that appeared "excessive and arbitrary".
"Both matters are receiving our attention," Eagles said.
He said pharmacists were expected to explain all itemised charges related to prescriptions, and patients had the right to consult their pharmacist on all fees levied.
A draft of the rules was published for comment in October 2003, was now being finalised and would be published soon.
