The Kalamazoo Gazette obtained a video showing the trooper leaving his cruiser with gun drawn, then handcuffing the woman and putting her in the backseat of his cruiser.
State police asked St. Joseph County Prosecutor John McDonough to investigate the April 15 traffic stop on U.S. 12 near Sturgis.
The Associated Press is not naming the trooper because he hasn't been charged with a crime.
In a statement, the prosecutor said he was "appalled and disgusted" by the trooper's actions. McDonough said he did not want the trooper "to have the opportunity to do anything like this again and certainly not in St. Joseph County."
Authorities say the woman was driving 77 mph in a 55 mph zone and stopped about 35 seconds after the trooper activated his lights and siren. They say she was rushing home because her father had called her to say that their home had been burglarized.
"I chased you for two miles with my lights and sirens at almost 80 mph. Do you see a problem with that?" he asked her.
"Yes, I do," she responded in the video recording. "I honestly didn't see you."
In a written statement to a supervisor, the trooper said he was thinking about the 2013 fatal shooting of Michigan state Trooper Paul Butterfield II during a traffic stop.
"With the recent incident ... at the forefront of my mind, I elected to 'clear' the vehicle for my safety as I feel the vehicle could have suddenly pulled to the side in an effort to lure me into a vulnerable position where I could easily be shot," the trooper said in the statement, which the newspaper obtained under a Freedom of Information Act request.
The trooper is on paid leave during the investigation.