The institute is encouraging charities to take part in the Postal Services Commission's consultation on the proposals.
It claims the structure would see charities miss out on millions of pounds of income. The institute also says that many organisations would be forced to choose between increased postage costs or reduced direct mail and donor marketing.
It wants Royal Mail to ensure that the cost to charities of sending an A4 letter or newsletter is not increased beyond the lowest-priced item of mail.
The institute is consulting its 200 member organisations on their views in order to form a well-represented response to the proposals. It intends to submit a report on its findings to the commission and MPs.