Faculty and students argue that many of the changes won't generate enough saving to justify the cuts.
The Journal Gazette reports the school's College of Arts and Sciences is most affected, with geology, philosophy and women's studies being eliminated Jan. 1.
Under the new agreement, the board of trustees from both universities must be presented with proposals for a new governance structure by December.
A new report recommends IU to maintain its health sciences and medical programs, but the campus would effectively become an extension of Purdue.
IPFW, a Fort Wayne campus managed by Purdue but jointly owned by Purdue and Indiana University, are in talks to change managements.
A study committee could recommend the legislature give Indiana University-Purdue University Fort Wayne more autonomy for funding and degree offerings.
Legislators will look at the best way to govern the nine regional campuses in a study committee this summer.