Payments to the FSCS remain a contentious issue to the building society, which has suffered a 69 percent drop in profits.
The amount big players pay to the savings compensation scheme is excessive, Nationwide has suggested.
Interim financial results from Britain's largest building society showed that profits had fallen by 69 percent. In comments accompanying the data release, the firm's chief executive said that net income had been dragged down by the £241 million paid to the Financial Services Compensation Scheme (FSCS).
Financial obligations to the compensation body have been ramped up over recent months, as the stability of the banking system has come under pressure in the financial crisis - putting more firms at risk of collapse. Under UK law, the first £50,000 of customer cash savings deposits will be compensated by the FSCS in the event of the account provider going into administration.
Several firms have sought out government bailouts, others have been forced into emergency takeovers and one Icelandic provider, Icesave, has gone under entirely.
Nationwide said that its financial obligations to the scheme were "unfair", as the amount each account provider has to pay into the FSCS varies depending on market share. The building society suggested that this system should be replaced by one which saw firms who faced the biggest risk of going under paying more than those who worked to a more prudent business model.
Chief executive Graham Beale said: "Nationwide has remained strong in the midst of all this turbulence and has been the only major UK banking institution not to raise capital or seek access to government sponsored capital enhancing schemes."
He added: "We regard the fact that the FSCS charge is not linked to the level of risk posed to the financial system by individual institutions, but instead is allocated by share of the retail savings market, as illogical and unfair, producing a disproportionate outcome for the low risk retail funded institutions, particularly building societies."
