Troy Woodruff resigned Thursday, a day before the state's Inspector General released a report clearing him of all wrongdoing on conflict of interest charges.
The state argued Monroe County's noise ordinance was delaying construction on Interstate 69.
The first phase of a $7.3 million project on S.R. 37 in Martinsville begins at 7 p.m. Friday.
Five companies, including Amtrak, have submitted proposals for how they can improve the rail line in an attempt to reduce costs while increasing ridership.
The state plans to upgrade State Road 37 to interstate standards by 2016.
The approved legislation releases $200 million right away but requires state budget committee approval for the second $200 million.
Most of Central Indiana is under travel advisories after this weekend's winter storm.
Many who live and work close to State Road 37 are concerned about the impact of impending construction.
A Senate committee scaled back the amount of money INDOT will receive form the Major Moves 2020 fund.
INDOT spokesman Nathan Riggs says they've used nearly seven thousand tons of asphalt and 8,100 employee hours to fill potholes so far this winter.