Badgers coach Bret Bielema said Phillips had exploratory surgery Friday and would need an additional procedure after the current school year was over.
"It kind of was reassuring to him, because I think he didn't feel overall that the knee was right, where it was at," Bielema said. "It kind of gives him some answers for him to move forward."
Bielema said Phillips may petition the NCAA for additional eligibility.
Bielema described Friday's procedure as minor and had hoped Phillips, who twice has undergone ACL surgeries, would be cleared by June. Phillips was expected to challenge Jon Budmayr for the starting quarterback spot in fall camp.
"It shouldn't be anything major, hopefully," Bielema told reporters following Thursday's practice. "Kind of just deal with the cards after they are there. If it's something they can take care of and clean up, hopefully, he'll be back full-time in June."
Phillips, who competed for Wisconsin's starting quarterback position in 2009, tore the ACL in practice in March 2010 and again in November. He has made a rapid recovery to participate in some drills this spring before the setback.
Adam Rittenberg covers Big Ten football for ESPN.com. He can be reached at email@example.com. Information from The Associated Press was used in this report.