Over 4,000 IFAs regulated by the Insurance Brokers Registration Council are set to contribute to the Investors' Compensation Scheme for the first time.
The Financial Services Authority is to include IFAs registered by recognised professional bodies such as the IBRC when it creates a super-compensation scheme next year.
Under the current rules, the 4,142 individual advisers registered by the IBRC escape paying ICS levies.
They could now be hit by an ICS bill amounting to several hundred pounds each. Some members fear the bills could force firms out of business.
Details of the new ICS are yet to be finalised and the IBRC still hopes to avoid coming under the ICS regime. It wants to maintain partial regulatory freedom.
Deputy registrar Alison Carr says: "We are looking for views from the Treasury and are holding talks with the FSA. But it is quite likely to happen although it is not set in stone."
IBRC member and Bridgland Insurance Brokers principal Tony Bridgland says: "This is another disgraceful move. The IBRC is to be swallowed up and we face paying enormous sums of money. If this is the case, it means members are facing great hardship because of the big boys doing wrong."
IBRC members pay a grant levy and a registration fee of about £850 a year to be regulated by the body. The size of fee depends on the amount of each IFA's investment business.