Attorney general Michael Lauber said the "suspicious" cases had been reported by banks and that a "huge and complex" inquiry into football's world body could take months if not years.
Officials said the 53 are individuals and companies and that each case could involve many more transactions.
"We note positively that banks in Switzerland did fulfil their duties to file suspicious activity reports," he told a press conference.
"Partly in addition to the 104 banking relations already known to the authorities, banks announced 53 suspicious banking relations via the Anti-Money-Laundering-Framework of Switzerland," he added.
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It is one of two major fraud investigations that have rocked FIFA.
US authorities last month charged 14 people in a separate bribery investigation.
Lauber said he "does not exclude" questioning FIFA boss Joseph Blatter or general secretary Jerome Valcke, although neither is currently under suspicion.
- Probe will take time -
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He said nine terrabytes of data had been seized, including at FIFA's Zurich headquarters and the probe would take time.