Rates are the property taxes paid by households and businesses.
Currently, charity shops are exempt but an official consultation has questioned whether that exemption should continue.
Robin Osterley, chief executive of the Charity Retail Association, said the imposition of full rates would cost the charity sector up to £5.5m.
He said this would mean that money "would no longer be available to charities to fund their vital life-saving and life-changing work".
Elsewhere in the UK, charities have their rates reduced by 80% leading the consultation to ask if Northern Ireland charities should "pay some rates".
The consultation has now closed and no decisions are expected until after the Northern Ireland Assembly election in May.
A coalition of charities has urged Northern Ireland's finance minister to reject a proposal that charity shops should begin paying rates.