An orchestra facing a £20,000 bill may have to increase ticket prices and cut shows to meet its debts.
The Brighton Philharmonic owes unpaid National Insurance (NI) contributions, which only recently came to light.
It is one of hundreds of orchestras nationwide which have discovered they have been under-paying contributions to the tune of £33 million.
General manager Ivan Rockey said: "It's unlikely this will put us out of business. It is thought about 80 per cent of orchestras are likely to face severe problems but if that's the case we're lucky enough to be in the other 20 per cent. It's not going to bankrupt us.
"It does worry me because it's going to be a huge payment followed by on-going payments. We will be paying more to the Government and less to our musicians. Consequently we will have to charge the public more to see our concerts or not have as many each year.
"If we put prices up will it put people off coming to see us?"
Debts mounted after the Government changed NI regulations in 1997 at the request of actors' union Equity.
Employers of freelance entertainers were told to pay higher contributions to cover the benefits claimed by resting actors.
Russell Jones, director of the Association of British Orchestras (ABO), said it was unaware the rules covered musicians until recently and discovered orchestras were liable just a few months ago.
Mr Rockey said it would be illogical to apply the rules to musicians because their working practices were different and they were rarely unemployed.
The Brighton Philharmonic may also have to pay about £5,000 extra a year if the regulations are not amended.
Worthing Philharmonic and the Sussex Symphony orchestras are not affected because they are not professional.
But Chris Cooper, secretary of Worthing Philharmonic, said all orchestras were finding it hard to make ends meet.
He said: "There is so much music available in the form of inexpensive CDs it makes it a very challenging environment for all orchestras.
"We have to pay royalties until 75 years after the death of the composer. Orchestras are getting hit on all sides and people may not bother any more."
The ABO, Arts Council England, the Department for Culture, Media and Sport and HM Revenue and Customs are meeting to tackle the crisis.
A leaked email between Mr Jones and orchestras' chief executives and finance directors warned the giant bill could bankrupt several big names including the Philharmonia Orchestra and the London Symphony Orchestra.
A look at five sample orchestras showed the payments would put four into liquidation.
Mr Rockey said: "The best solution would be to alter the wording of the rules so musicians are not included."
An HM Revenue and Customs spokeswoman said: "To guarantee access to the widest range of contributory benefits possible, our policy since 1998 has been to treat orchestra members as employees for NI contribution purposes.
"We have an excellent track record for agreeing time-to-pay arrangements. It is our policy to support any business or organisation that experiences temporary cash-flow difficulties. We do not believe any orchestras will need to close.
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