The Yorkshire, Leeds and Skipton building societies have all hit out at the "disproportionate" costs that they must pay under the financial services compensation scheme.

Two of the building societies said the scheme affects their ability to offer well-priced products to customers and warned that members would have to pay for the bailout.

The cost to the building society sector over the next three years of the Government-backed scheme is estimated to be £600m.

Iain Cornish, the chief executive of Yorkshire Building Society, said: "Fundamentally, building societies as a whole have operated their businesses in a way that is much more prudent than the banks.

"But the consequence of operating that prudent model is we will get a disproportionate share of the bail-out costs from B&B.

"I have no objection to being part of a compensation scheme and paying a share of that. But the amount should be risk-based. Lower risk institutions should pay a smaller share."

Ian Ward, the chief executive of Leeds Building Society, called for the financial services compensation scheme to be reformed.

He said: "We need to come up with a better solution.The scheme was never designed for these big events. Keeping a vibrant building society sector is essential."

The Government stepped in to nationalise Bradford & Bingley at the end of September as the bank edged towards collapse.

The Government took B&B's mortgage book into public ownership and sold its savings business and branch network to Spanish banking group Banco Santander.

The transfer of the retail deposits was largely guaranteed by a £14bn loan to the financial services compensation scheme.

The Government hopes that mortgages and profits at the nationalised B&B will eventually repay the loan itself while UK financial institutions – the members of the scheme – must repay the interest on the loan over the coming years.

Building societies say they must pay a larger slice of the interest because of the way the compensation scheme is calculated.

Under existing guidelines, the societies argue the size is determined by the amount of retail deposits an institution holds at the end of each December.

Building society chiefs say this system favours the institutions that pursued riskier models and relied on wholesale money markets to fund their busi- ness.

David Cutter, the deputy chief executive of Skipton Building Society, said: "There is a growing anger. It's a bit galling that the sector which has adopted a far safer business model is paying a higher cost to bail out failed banks."

He added: "We are picking up a disproportionate element of the costs to fund the bail out. It will have a significant impact on societies' results because the figures are quite significant.

"That means it has to be paid for by the members which means in terms of being able to offer the most competitive mortgage and retail rates we have to take that considerable cost into account."

He questioned what would happen if there is a shortfall in the repayment of the B&B loan.

The financial services compensation scheme underwrites up to £50,000 of retail deposits, rising to £100,000 for joint accounts.

Mr Cornish said the scheme was never intended to operate with sums in the scale of the B&B bail-out.

He said the rescue plan was "done in a hurry" to stabilise a dangerous situation "and to not think of the broader consequences".

Mr Cornish added: "Now it's happened it seems sensible to me that people should reflect a little more on the consequences and just finesse some of the arrangements so they are not potentially damaging to the very institutions that have done least to cause the problem that the financial services sector has got into."

Mr Ward pointed out that no taxpayers' money had ever gone into rescuing a British building society and said any "local difficulty" has been sorted out within the sector.

He said the compensation scheme should be pre-funded and warned that more financial institutions would be entering the high street seeking retail deposits as the wholesale money markets contract.

He added: "There has got to be some action on pre-funding.

"You can't just get let into the club without paying some money into the central pot to start with. Otherwise... it restricts our abilities to offer attractive mortgages and savings rates."