In April, the Central Bank of Moldova discovered that the three banks in question granted loans worth a total of $1 billion, equal to 15 percent of the impoverished ex-Soviet state's GDP.
The beneficiaries of the loans have not been identified, but the money appears to have been spirited away.
According to a parliamentary committee's report, leaked to the press, some of the money is believed to have landed up in Russian banks.
The transactions apparently happened over the course of several days, just before parliamentary elections late last November, in which pro-European Union parties narrowly squeezed pro-Russian representatives out of the majority.
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Prosecutors and American auditors have been searching the banks' books for clues about the mysterious transactions, an embarrassment for the ex-Soviet state on track for EU membership.
The scandal has threatened to destabilise the whole banking system in the country of 3.5 million people.
The protesters chanted anti-corruption slogans, and called for the resignation of the prosecutor general, several Supreme Court judges and politicians they believe were involved in the scandal.
Moldova's prosecutor general has launched a probe and two people, whose identities have not been disclosed to the public, were detained while others have had their funds frozen.