The FSA's application fees for authorisation published last week are "disproportionate" and could lead to job losses, according to brokers.
Despite the insertion of a new band for firms with annual income of between £1m and £3m, there were complaints that the FSA had not gone far enough.
Eastern Alliance chief executive Grant Taylor said: "It still leaves the small to medium sized business bearing a disproportionate amount of the costs. The leap in fees between the lower and middle bands remains enormous and seemingly beyond any reasonable justification.
"The final document does nothing but confirm the basic inequality of what was proposed in CP180."
Biba regulatory working party chairman Chris Arter said: "There is a big danger that firms might restructure to get into a lower band. Unprofitable parts of a business might be removed, leading to job losses."
The document also addressed the issue of annual fees. But uncertainty remained for brokers as the FSA failed to clarify the level of these fees.
IIB director general Andrew Paddick said: "The FSA has said those falling in the £1m application fee bracket will not necessarily be in the lowest annual fee band. But it has not said how much it will be."