State budget director Adam Horst says department commissioner John Eckart will step down after seven years leading the agency.
Speaking at a Thursday news conference, Horst blamed the problem on a programming error.
The revelation of mishandled revenue follows news late last year that some $320 million in corporate taxes collected over four years had not been transferred to Indiana's general fund.
The revenue department says the mishandled money will be distributed with interest to the 91 of Indiana's 92 counties that have local income taxes. An outside audit will be conducted of the agency's procedures.
