President Barack Obama waves as he arrives to deliver the commencement speech during the 2009 graduation ceremony at the University of Notre Dame. Catholic colleges across the nation are dealing with the aftermath of Notre Dame’s decision to have Obama speak.

The protests over the University of Notre Dame’s commencement invitation to President Barack Obama will have an impact beyond the South Bend campus and far longer than graduation season.

While the drubbing focused on the nation’s most prestigious Roman Catholic school, the criticism also served as a warning to all Catholic colleges and universities about the potential for opposition to their own policies.

The U.S. Conference of Catholic Bishops has said that Catholic schools should not give awards or platforms to those who “act in defiance of our fundamental moral principles.”

“There have occasionally been tensions between an individual bishop and a Catholic institution within his diocese, usually related to some public misrepresentation of or dissent from Catholic teaching, or some professor considered to be at odds with the church’s doctrine, but nothing of this scale,” said the Rev. David O’Connell, president of The Catholic University of America, which was founded by the nation’s bishops.

“When one of the more prominent Catholic institutions does this, the bishops grow concerned that it will signal approval or the perception of approval of such contrary positions, and that other Catholic universities or colleges will follow suit.”

Obama, who supports abortion rights, received standing ovations when he was awarded an honorary degree and gave the Notre Dame commencement address last Sunday.

Still, the unprecedented clamor in the weeks leading up to the event emboldened watchdog groups. As just one example, the Cardinal Newman Society, an independent Catholic organization that monitors Catholic colleges and universities, said it collected more than 367,000 signatures for an online petition condemning Obama’s role in the ceremony.

“Given the high-profile nature of the Notre Dame situation, one would think these colleges and universities would back off anyone problematic,” said Patrick Reilly, the society’s president.

Even more importantly, the nation’s bishops showed a new willingness to speak out when they believe a decision by a Catholic college or university undermines the church.

Bishops generally stay silent and defer to a local prelate about any trouble inside his own diocese, including conflicts with schools in his jurisdiction. Yet, more than 75 of the roughly 265 active U.S. bishops criticized Notre Dame for honoring Obama. Outside the Notre Dame graduation, Bishop John D’Arcy of Fort Wayne-South Bend, Ind., who boycotted the event, celebrated a Mass at a rally for anti-abortion protesters.

“This is an impact that is likely to be felt for some period of time,” said Richard Yanikoski, president of the Association of Catholic Colleges and Universities, which is based in Washington and represents more than 200 U.S. schools. “It’s certainly — but one doesn’t know exactly how — helping to shape public perception.”

The board of the college association will discuss commencement speakers in light of the Notre Dame controversy in a meeting next month. Yanikoski, a consultant to the U.S. bishops’ education committee, expects the panel will also take up the issue, although probably not until their next scheduled meeting in November.

Tensions have erupted regularly among the schools, bishops and Catholic activists since 1967, when Catholic academics released the “Land O’Lakes Statement on the Nature of the Contemporary Catholic University.” The leaders affirmed the colleges’ role of serving the church but declared some autonomy from the Catholic hierarchy, so that the schools could be guided by professional leadership, not just the religious orders that created them.

“In the earlier period, people didn’t think, ‘What does it mean to be a Catholic university? What is the mission of a Catholic university?’ It was foregone,” said William Portier, a theologian at the University of Dayton, a Marianist school in Ohio. “But after the 1960s, it was important to reflect on that.”

In 1990, Pope John Paul II released the document “On Catholic Universities,” saying the schools must adhere to church teaching on faith and morals. The Vatican took further action in 2002, requiring theologians at Catholic schools to receive a “mandatum,” or mandate, from a local bishop, attesting that they follow church doctrine.

Yet, the debate usually flares most dramatically during commencement season.

As a result, the nation’s most prominent Catholic lawmakers who support legalized abortion in any way often find themselves without an invitation to a Catholic college graduation. The Cardinal Newman Society has said the number of protests launched over commencement speakers has dropped from 24 in 2006 to 13 in 2007, then to eight last year. In several cases, the invited speaker withdrew in response to the opposition.

This year, Archbishop Alfred Hughes of New Orleans boycotted commencement at Xavier University because the university honored Donna Brazile, a Democratic strategist who supports abortion rights.

Bishop Joseph Martino of Scranton, Pa., condemned the choice of U.S. Sen. Bob Casey as graduation speaker at King’s College in Wilkes-Barre. Martino called it “an affront to all who value the sanctity of life.”

The Pennsylvania Democrat opposes abortion rights, but Martino has criticized him for voting to confirm Kathleen Sebelius as Secretary of Health and Human Services. Sebelius, a Catholic, supports legalized abortion. Casey voted to confirm her because he believed it would be irresponsible to leave the health position vacant, his spokesman has said.

Yanikoski said that most schools in his association have full-time mission officers who help guard Catholic identity on campus, including strengthening the review of major honorees. However, he noted that “the bishops have become much more sensitive to this matter” in recent years, leading to conflicts such as the one at Notre Dame.

Patricia McGuire, president of Trinity Washington University, which was started in the nation’s capital more than a century ago by a women’s religious order, condemned the “hostile” reaction to Notre Dame’s honor for the president in her commencement speech last weekend.

“The terrible danger of the siege at Notre Dame, and the ugly specter of Catholic vigilantism’s efforts to intimidate Catholic academic leaders and politicians is that Catholics will be driven back to the edges of American life,” she said. It “will affect the future of all Catholic colleges.”