The NCAA on Wednesday cited Oregon for failing to monitor its football program, placing the team on probation and marking the quiet end of the association’s lengthy and high-profile investigation.

The infractions committee found that Chip Kelly, the team’s former coach, who is now the coach of the NFL’s Philadelphia Eagles, had not adequately supervised the program, and penalized him by putting up conditions on his return to the college ranks, should he try to return.

The investigation, which began well over two years ago, centered around Oregon’s ties to a recruiting service provider, who assisted the university’s football program in trying to woo multiple players to the team.

The committee’s report said that the provider gave cash and lodging to a prospect and violated other NCAA rules through calls and contacts.

“This case involved major infractions of NCAA legislation committed by the recruiting service provider, who became an athletics representative, in addition to violations committed by institutional staff members, most notably, the former head coach,” the committee’s 30-page report said.

According to the report, Oregon’s football program paid the recruiting service provider $25,000 in 2010. The committee report did not name the provider, but he has been identified in news media reports as Will Lyles, a Texas-based scout. He could not reached for comment.

Oregon said in a statement that the NCAA’s findings were consistent with what the university had recommended, based on its own review.

“Throughout this process, there has been speculation and innuendo regarding the nature and severity of potential violations, much of which was unfounded,” Rob Mullens, Oregon’s athletic director, said in a statement. “As stated by the NCAA Enforcement Staff, the violations committed in this case were unintentional.”

The committee issued a series of penalties, including the three years of probation, the loss of a scholarship, and a ban on subscription to recruiting services — but stopped short of barring the school from participating in postseason bowl games.

“The sanctions were pretty lenient,” said Justin Sievert, senior counsel to Michael L. Buckner Law Firm in Pompano Beach, Fla., which specializes in enforcement cases. “You don’t have a lot of penalties that have a lot of teeth.”

Sievert pointed to the punishment of Kelly, who is preparing for his first season as coach of the Eagles.

The committee found that Kelly was unaware of the use of the recruiting service and its conduct, but cited him with an 18-month show-cause penalty under the view that “it is the head coach’s responsibility to know NCAA rules and regulations and to see that every coach and staff member complies with those regulations.”

During the show-cause period, if any university in the NCAA wishes to hire Kelly for an athletics role, both the university and Kelly must appear before the infractions committee — a point that was probably made moot by Kelly’s taking the helm of the Eagles in January.

“Everybody knows he is employed by the Philadelphia Eagles right now,” Sievert said. “Most people are pretty confident he is not going to be fired by the Eagles in the next 18 months.”

On a call with reporters, Gregory Sankey, the associate commissioner of the Southeastern Conference and a member of the committee on infractions, refrained from answering critics claims that the punishments were “toothless.”

“I’m not going to go through a dental exam,” Sankey said, adding the penalty is “meaningful,” even if someone is no longer with a university.

Kelly, in a statement issued through the Eagles, apologized to the university and its fans. “I accept my share of responsibility for the actions that led to the penalties,” he wrote, adding that the investigation did not have a role in his decision to leave the university.

“I do expect the University of Oregon and its football program to continue to thrive at a high level,” Kelly wrote. “They are a talented and resilient group of coaches and players and I’m sure they will attempt to put today’s news behind them very quickly and move forward as they prepare for the 2013 season.”

The team Kelly left behind is coming off a 12-1 season, capped by a victory over Kansas State in the Fiesta Bowl. Before his departure, Kelly led Oregon to four straight Bowl Championship Series games, including a loss in the BCS national championship game in 2011. Oregon is expected to field another Top 10 team in 2013.