INDIANAPOLIS (AP) — The NCAA’s home-grown scandal is hitting hard at headquarters.

President Mark Emmert announced Monday that Julie Roe Lach, the vice president of enforcement, is leaving and will soon be replaced by private attorney Jonathan Duncan after her role in the botched investigation at the University of Miami. He even suggested the NCAA’s board of directors and executive committee could hold him accountable for this mess, and it’s not over yet.

After releasing a 55-page report detailing how the NCAA violated its own practices and policies by paying the attorney for convicted Ponzi-schemer Nevin Shapiro thousands of dollars to help with the Miami case, Emmert spent more than an hour doing damage control on the latest black eye to hit the organization.

“I think the damage is, first of all, for those people who were already skeptical or cynics, this feeds into their cynicism,” Emmert told The Associated Press after a conference call with other reporters. “For those of us who have great confidence in all the people around this building, it’s painful to have to deal with an issue that fails to live up to our standards and expectations. I think that’s the challenge for all of us that work here.”

The report, written by attorney Kenneth L. Wainstein, details how now-former NCAA investigator Ameen Najjar appeared to manipulate the process by hiring Maria Elena Perez, Shapiro’s attorney, to help the NCAA obtain information from a bankruptcy proceeding — information that would have otherwise been unavailable. Shapiro has said that it provided improper benefits to dozens of football and basketball players at Miami.

According to the report, Lach obtained clearance for paying Perez, but the NCAA’s legal staff nixed the idea. Najjar then contacted Perez himself with what the report describes as a “way around” the road block.

The report said Najjar, who left the NCAA last spring, assured Lach and Tom Hosty, the managing director of enforcement, that the legal staff had approved the deal when it had not. Najjar did not return phone messages Monday night.

The NCAA didn’t figure out what happened, the report said, until Perez billed the NCAA $57,115 for hours in August. By that time, the NCAA had already paid out approximately $10,500 to Perez in expenses.

Wainstein called Lach cooperative and said nothing the external investigators found called her integrity into question. Lach did not immediately respond to a message left by The Associated Press on her cellphone.

“The actions we are taking today are clearly consistent with holding people accountable for their behavior,” Emmert said. “If the executive committee believes some disciplinary action needs to be taken toward me, then I’m sure they will.”

The incident has been an embarrassing blow to the NCAA, which is fending off a number of lawsuits and is the target of sharp criticism in some quarters for the penalties it handed to Penn State following the Jerry Sandusky child sex-abuse scandal. And Wainstein will now embark on the second part of the investigation, which could include looking into previous NCAA infractions cases and suggesting ways to prevent another rogue case.

“I don’t have any specific recommendations now,” Wainstein said. “But as President Emmert said, I’m a former prosecutor and I’ve managed prosecutions and investigations for the better part of 20 years, so I’m going to suggest some ideas that I import from that context.”

Emmert already has two new ideas.

He suggested putting together a committee to hear what amounts to a preliminary case before moving forward, and perhaps adding an ombudsman to the NCAA staff. Emmert later said he’s not sure how that would work though he acknowledged an ombudsman would need some power.

There are more immediate concerns, too.

Lach is expected to leave March 1 and over the past 18 months has been closely involved with creating a new enforcement structure. The new multi-tiered penalty approach was approved in October, and the first part of the NCAA’s revised rulebook was backed last month at the NCAA’s annual convention.

A second part or rules changes is expected to come sometime after April’s quarterly board of directors meeting.

Now, though, Emmert wants school leaders to provide more input about enforcement policies.

“We need to be able, at the same time, to say OK as we’re changing these rules, how do want them enforced? What approach to enforcement can we abide by?” he said.

That’s where Duncan could help. He’s a private attorney who has spent the last 15 years focused on sports law and education.

“We need to bring in expertise, like in the case of Ken, he’s a prosecutor and has an approach that’s very different to what we have in a voluntary association, but we need people with those various perspectives that can come to us,” Emmert said. “That’s one of the advantages of having John. John knows this world very, very well and will bring a very balanced perspective to the whole regulatory process.”

How hard will these changes be at the NCAA’s home office?

One of Emmert’s first moves after taking office was promoting Lach in October 2010 from director of enforcement to vice president of enforcement, the first woman to hold the job. At the time, Lach promised to change the way the NCAA did business, offering more transparency about how investigations were handled. She delivered in part by setting up mock investigations for media members.

But she also presided over one of the most tumultuous times in NCAA history.

Lach was hired by the NCAA in 1998 as a student-athlete reinstatement representative after one year as an intern. She was named director of student-athlete reinstatement in 1999 and director of enforcement in 2004. She also spent nine years on the board of trustees at Millikin University, her alma mater.

Late last year, the Los Angeles Times reported that an NCAA investigator had been fired after her boyfriend had been overheard on a flight saying that the NCAA would never allow highly-touted recruit Shabazz Muhammad to play. Lach was on maternity leave when the investigator was reportedly fired.

And since last summer, two investigators have left, director of enforcement Bill Benjamin resigned and now Lach is on her way out, too.

“This is an outcome that nobody wants to see on their watch or anyone else’s,” Emmert said. “It’s something that’s an embarrassment to the association, it’s something that’s contrary to all the things we engage and all the things we espouse, so this is not a good situation at all.”

NCAA President Mark Emmert. (Associated Press)

Michael Conroy