The crash took place on Marzane Road south of County Road 400 West.
He was wanted for Probation Violation and Failure to Register as a Sex Offender.
The department said Madison may be in the Decatur, New Haven or Huntington areas with friends or people "assisting in hiding her."
The crash was reported around 9:15 p.m. on U.S. 224 and County Road 300 West.
The burned body of Owen Collins of Bluffton was found in a rural area Jan. 18 after Arnold reported him missing.
Police found him hiding near a tree, covered in blood and holding two large kitchen knives.
Indiana Governor Mike Pence traveled to that area, along with Huntington and Wells counties. He met with first responders and surveyed the flooded areas
Officers went to an apartment in the 300 block of Lamar Street around 3:15 p.m. and found the woman bleeding from her neck and arms.
The deer entered the school though a window and spent about 30 minutes in the classroom.
Police have not released details about the circumstances leading to his arrest.