In total, more than a dozen Spanish banks received €76.14 billion ($85.2 billion) in capital injections and financial guarantees as the sector struggled under the weight of the worldwide financial crisis and a property bubble burst in 2008.
The capital injections were implemented via FROB, the state's bank restructuring fund.
This fund injected 54.35 billion euros, of which 41.3 billion euros came from EU rescue loans in 2012.
But according to the central bank, 39.5 billion euros may never be paid back, which means the state will only recover around 28 percent of its capital injections, even as it continues to reimburse the EU for the bailout.
It did not detail how it made its calculations, nor why the state would not recover that money.
But banks have been plagued by toxic assets they inherited during the crisis - property taken from individuals or developers unable to reimburse their loans - which they are having difficulty selling off.
Spain's banks were hit hard by the worldwide crisis.
Within just a few months, as more and more people lost their jobs and were suddenly unable to pay back their mortgages, banks quickly found themselves in difficulty and the government was eventually forced to step in.
The situation prompted a wave of mergers and acquisitions in the sector, which saw the number of savings banks drop from 45 to just 15 in three years.
Prime Minister Mariano Rajoy pledged in 2012 that the European banking rescue would not cost "one euro" to the taxman.
A central bank spokesman said, however, that the estimates were not completely definite.
The final amount will depend on what the state recovers when it sells its stakes in entities it had to step in and help during the crisis, such as Bankia.