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.