Wagner disclosed the off-book accounts at a Thursday press conference, but says she hasn't found evidence of abuse, fraud or mismanagement.
A secret Pittsburgh police expense account triggered an investigation earlier this year.
Wagner says she is working with county manager William McKain to move the accounts from 10 different departments into the central computer system, where they can be tracked.
Most of the accounts are relics of an earlier age, when the county's cumbersome central accounting system frustrated departments enough to open their own bank accounts. In many cases the accounts hold fees and taxes that are owed to other agencies but temporarily held in county custody.