"My office has opened a fraud investigation," Rhynhart said.
According to the report, the discrepancy dates back several years. The report states other city accounts have not been reconciled by the Treasurer's Office, some since 2010.
"We don't know at this point if it is fraudulent or just was put into the wrong account and can't be found, but we need to address it with urgency," said Rhynhart.
The report goes on to say sloppy bookkeeping led to $924 million in accounting mistakes.
"The city's finance department accountants fixed it once we brought it to their attention, but that's not the way it's supposed to work," she said.
Mayor Jim Kenney said the money isn't missing.
"It's like your checkbook, you have to balance it every month and it hasn't been balanced in a while," he said. "It's not something we want, it's not something we necessarily caused, but we are fixing it."
An outside accounting firm will go through the city receipts for every single day over the course of the past three years. The mayor has also created a reconciliation task force to address the problem.
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