PHOENIX >> NCAA President Charlie Baker says Michigan won the national championship “fair and square” and defended his decision to inform the school and the Big Ten during the season that the association’s enforcement staff was investigating allegations of an in-person scouting and sign-stealing scheme.

The top-ranked Wolverines beat No. 2 Washington to win the College Football Playoff on Monday night, capping a perfect season, the back half of which was shadowed by the NCAA investigation and led to the Big Ten’s three-game suspension of Michigan coach Jim Harbaugh.

In a meeting with reporters, Baker explained why the NCAA took the unusual step of informing parties involved in the investigation last October.

“We were approached by a third party, who said they had evidence that Michigan was involved in a very comprehensive and unusual sign-stealing scheme,” Baker said late Tuesday. That party was told they needed to come in person to NCAA headquarters in Indianapolis to present evidence to enforcement staff as part of a vetting process.

“They did and they showed it to our infractions people and it was very compelling,” Baker said, giving no details of the third party’s identity.

Baker said because of the potential to impact the outcome of games, the NCAA decided to contact the Big Ten and Michigan and share the first pieces of what it had received from the third party.

The Big Ten then informed schools that had played Michigan and schools that were still left on Michigan’s schedule. Soon after the news leaked to the media and the Big Ten and Michigan both publicly acknowledged the investigation. Harbaugh, who is facing unresolved NCAA violations in a separate case tied to recruiting, has denied any knowledge or involvement in impermissible scouting of opponents and he again declared his program innocent of wrongdoing after beating the Huskies.

Baker said he was confident the NCAA did not leak any information to the media about the investigation.

“I don’t regret doing it because sitting on that information, I think we would have put everyone, including Michigan, in an awful place,” Baker said. “As it was, it was out in the public domain. And people either made adjustments or didn’t. And at the end of the day, no one believes at this point that Michigan didn’t win the national title fair and square. So, I think we did the right thing.”

The NCAA sign-stealing investigation is likely to last many more months. Michigan has not yet received a notice of allegations from the NCAA, formally detailing the accusations, and will have 90 days to respond once it does. A hearing in front of the infractions committee would need to be scheduled after that.

“We do have a series of discussions going on with the infractions folks about whether or not we can’t do some things to speed up the pace of our investigations,” Baker said. “Because certainly in a case like this you’d like to be able to move a lot more quickly.”

Potentially complicating the Michigan situation is the uncertainty of Harbaugh’s future with the Wolverines. Harbaugh has said repeatedly he had no involvement of any sign-stealing operation, which involved people allegedly being sent to games involving Michigan opponents to video record signals coming in from the sideline.

Records from other Big Ten schools show former Michigan recruiting analyst Connor Stalions bought tickets to numerous games involving future opponents. Stalions was first placed on leave by the school and then later resigned.

Baker would not speculate on a timetable for the Michigan case or on whether the NCAA would potentially share the findings of its investigation with any NFL team interested in hiring Harbaugh.

Michigan is still embroiled in a separate NCAA case involving football recruiting infractions and Harbaugh failing to be forthright with investigators. The school received a notice of allegations on that case in December. Michigan self-imposed a three-game suspension on Harbaugh at the beginning of this season, trying to mitigate future penalties after an attempt to settle the matter was rejected by the NCAA Committee on Infractions.

Baker did not attend the College Football Playoff championship game in Houston, but said he watched and found Michigan to be “clearly the better team.”

“I said before that part of the reason I thought it was important to talk to the Big Ten and to Michigan about this was it might affect the outcome of games,” Baker said “And I don’t believe at the end of the season it did. And I think that’s important.”