The banks and building societies covered by the government guarantee scheme are paying less than half the expected costs originally forecast by the government, it has emerged.

The institutions together paid just €295m for the first nine months of the guarantee, despite the government's initial estimate that the scheme would cost €1bn, or €250m per quarter, Department of Finance figures show.

The seven institutions covered by the bank guarantee scheme are expected to place their fourth quarter payments into the mandated account to pay for the government's protection up to its first anniversary in September.

If they maintain their current rate of payment, the government will recoup just under €400m of its costs for underwriting the banks' bonds.

The bank charge is supposed to cover the long-term costs of borrowing the exchequer incurred by the provision of the guarantee, which has led bondholders to demand higher premiums on Irish government debt. The additional costs were put at €1bn.

Finance minister Brian Lenihan said the fees paid to date have been less than first estimated because the charging model originally included €90bn in deposits that are actually covered by the enhanced deposit protection scheme, which is funded through a separate mechanism and does not affect the state's bond spread or debt rating.

The minister also said the total amount of liabilities is adjusting downwards as bank balance sheets shrink through the normal course of business.

However, subtracting the €90bn in deposits from the €450bn in total liabilities should only reduce the bill by 20%, while bank balance sheets are adjusting at an even slower rate.

Lenihan said the charging model is currently under review by the Department of Finance "and other stakeholders" to make sure the state ultimately recovers the total cost of the guarantee, suggesting banks may have to pay more later to make up for the shortfall or that the bond prices may come down over time.