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"We are not so interested in the motive but we want to be sure of the origin of the money," spokesman Vincent Derouand said, adding that neither throwing money away nor blocking a toilet was a crime.
The Tribune de Geneve newspaper, which first reported the unusual deposit, said the first blockage occurred in the toilet serving the vault at UBS bank in Geneva's financial district, and three nearby bistros found their facilities bunged up with 500-euro notes a few days later.
Derouand said two people had agreed to compensate the restaurants for the costs of the blockage, and the restaurants had withdrawn a complaint that they made when the incident happened in May.
The cash was confiscated during the investigation and it was unclear who would get it if it was found to be lawful. There was no immediate reason to think it was dirty money, Derouand said.
The European Central Bank said last year it had decided to discontinue the 500-euro note because of concerns that it was being used too often for illicit activities including money laundering.
A UBS spokesman declined to comment.