Still, Robert Barchi has the support of the state's most important politician, Gov. Chris Christie, who said Tuesday that he has "absolute confidence" in Barchi and won't meddle in university business, including its decision to hire Julie Hermann as athletic director.
There have been revelations in recent days that volleyball players at the University of Tennessee complained that Hermann abused them verbally and emotionally when she coached there in the 1990s and that she was involved in a sexual discrimination lawsuit while she was an administrator at Louisville. She was hired by Rutgers May 15 and is scheduled to start there June 17.
"I understand that there are some people that feel differently about it. It doesn't matter," Christie said during a testy moment in his monthly call-in show on TownSquare Media Tuesday night. "What matters is: What did the administration at Rutgers believe?"
Christie said he had talked with Barchi, the university's lawyer and the chairman of the Board of Governors and believes they should be allowed to run the university as they see fit.
"These are their decisions," Christie said. "Now they have to deal with the questions that are being raised."
Last month, Christie, a Republican, gave a similar view when some Democratic lawmakers first questioned whether Barchi should be president at the start of a cycle of problems in the athletic department. Then, the university fired basketball coach Mike Rice days after a video was made public of him berating players with gay slurs, kicking them and throwing basketballs at them.
The university's athletic director and top in-house lawyer both resigned under pressure. Since then, the university has defended its hiring of new basketball coach Eddie Jordan after the school said he was a Rutgers graduate when he was not. Lacrosse coach Brian Brecht was also suspended two games for verbally abusing his players during practice, something the university discovered in a probe of all its sports programs after Rice's dismissal.
In his defense of Barchi in April, Christie said it would be a mistake to let Barchi go because of his role in trying to rebuild Rutgers.
Lawmakers last year adopted a version of Christie's plan to reconfigure the state university system with the goal of making Rutgers into an elite medical science research center by having it absorb parts of the University of Medicine and Dentistry of New Jersey.
As the change was being planned, the school hired Barchi away from Philadelphia's Thomas Jefferson University, a medical school, to oversee the transformation and lead the creation of a strategic plan for Rutgers' future.
During a university Board of Governors meeting last month, an alumnus asked the board to bring back Tim Pernetti, the former athletic director; basketball players had a news conference; members of other sports teams protested; and TV networks' satellite trucks lined the street near the meeting. But Barchi's main presentation to the board was not about the aftermath of the Rice situation. Instead, he gave a detailed report on the process of gathering information to draft a strategic plan.
State Senate President Stephen Sweeney, a Democrat, said Tuesday that he would not say whether he thinks Barchi should resign until after he gets more details from him on Hermann's hiring.
Sweeney was not as convinced that only Barchi can oversee the transition to running medical schools. "The merger's going to happen regardless of whether Barchi's there or not," he told The Associated Press.
Rutgers is to take over the medical schools on July 1.
Barchi, 66, who had previously been a top administrator at the University of Pennsylvania, lacked experience running in the high ranks of a university with the athletic ambitions of Rutgers, where the football team has been transformed from perpetually mediocre to a regular in bowl games and where some faculty, students and alumni have fretted about the consequences of trying to have a big-time sports program.
Because of its stronger football program, solid academic reputation and location in the New York City media market, the university is set to join the Big Ten Conference in 2014.
The athletic directors at the conference's two most prominent schools - Ohio State and Michigan - said the problems in Rutgers' athletic department do not seem so damaging as to derail the university's entry into the league.
On his radio show, Christie also warned against a "character assassination" of Hermann, whom he said he does not know and has never met.
Meanwhile, some former colleagues came to her defense.
Joan Cronan, women's athletic director emeritus at Tennessee, said in a statement that she holds Hermann in high regard, and that while the ex-coach's tenure in the 1990s "was a very frustrating time for everyone connected with the volleyball program, I do not recall it being an abusive situation."
Marc Gesualdo, a graduate assistant for Tennessee's sports information department from 1994-96, attended virtually all of Tennessee's games during that stretch, but he wasn't at all practices.
"Never did I see anything that I would deem as inappropriate," he said, "or just like so outlandish that it was bordering on abuse."
Mulvihill reported from Haddonfield. Contributing to this report were Associated Press sports writers Tom Canavan in Newark, Teresa M. Walker in Nashville, Tenn., Rusty Miller in Columbus, Ohio, Larry Lage in Detroit, and Eric Olson in Omaha, Neb.; and AP writers Steve Megargee in Knoxville, Tenn., and Angela Delli Santi in Asbury Park, N.J.