ROME — The Vatican announced yesterday that it was disciplining the Mexican founder of an influential Catholic order after an investigation into decades of allegations that the now-elderly priest sexually abused boys in his care.

Marcial Maciel appears to be the highest-ranking priest to be sanctioned in an abuse case. Maciel enjoyed protective support from the late Pope John Paul II for many years, but Pope Benedict XVI, in his first major decision in the church's sex-abuse scandal, put aside his predecessor's wishes.

Maciel has denied the allegations in the past, and his organization, the Legion of Christ, repeated that position yesterday.

A Vatican statement said Maciel, 86, has been instructed to refrain from all public ministries and to adopt a "life of prayer and penitence." Experts said the Vatican's decision indicated that church investigators believed at least some of the accusations.

Given his advanced age and frail health, the statement added, Maciel will not be prosecuted under canonical law.

The Vatican said Benedict, who has vowed to rid the church of the "filth" that sexual abuse represents, personally approved the sanctions that were determined by his successor as head of the body that led the inquiry, the former archbishop of San Francisco, Cardinal William Levada.

Despite persistent rumors about Maciel's behavior for decades, the case against him took years to advance in the Vatican's labyrinthine legal bureaucracy. Eight men accused Maciel of sodomizing them when they were students under the priest's supervision in the mid-1940s to the early 1960s. Most of the accusers were Mexican, some as young as 10 years old when their alleged ordeals began.

An investigation was suspended by then-Cardinal Joseph Ratzinger in 1999. But Ratzinger reopened the inquiry after church investigators received testimony in late 2004 and early 2005 from at least 20 new accusers, who asserted that they were abused by Maciel well into the 1980s, according to the National Catholic Reporter.

Advocates for victims of pedophile priests praised the decision but said they had hoped Maciel would be banished from the clergy.

"It would have been easy to let this case quietly go unresolved, as so many similar cases have," David Clohessy, national director of the U.S.-based Survivors Network of those Abused by Priests said. "One positive move, however significant, doesn't constitute or guarantee a trend. While it may be tempting to assume this is a sign of progress yet to come, our painful history has taught us to be cautious and to err on the side of prudence."

Some of the original whistle-blowers were less pleased, saying the punishment was inadequate to the harm done and was woefully overdue.

The Legion of Christ was founded by Maciel 65 years ago. It is one of the fastest-growing in the world, claiming today 600 priests and 2,500 seminarians in 20 countries. Its lay branch, the Regnum Christi Movement, claims tens of thousands of members. Legionaries say they have established or run more than 100 schools.

Its traditionalist bent and fierce loyalty to the papacy earned it steadfast admiration from John Paul and other senior church officials. In four of John Paul's trips to Mexico, Maciel was at his side, the pontiff lavishing praise on a priest he called an "efficacious guide to youth."

Maciel had a turbulent childhood in Mexico that made him appealing to the conservative church hierarchy. He was a descendant of the so-called Cristeros, Catholic rebels who fought Mexico's revolutionary and anti-clerical government in the early 1900s. His uncle, Jesus Degollado Guizar, was the last commander-in-chief of the Cristeros army.

"I sometimes saw my mother with a rifle in her hands to defend us in case of an attack on the house," Maciel told the Catholic news agency Zenith three years ago. "I saw many dead Cristeros hanging from the lampposts, strung up by government troops. ... We saw our friends and neighbors hanged or shot in the town square. In my simple logic of a child I would tell myself that they had given their lives for Christ and were now with him in heaven. I too wanted to give my life for him."

Juan Vaca, a former priest who directed the Legionaries' U.S. headquarters, first notified Vatican officials of Maciel's actions in a letter to the pope in 1978, according to Jason Berry and Gerald Renner, authors of a book on Maciel and pedophilia among priests. Vaca's letter was never answered, the authors say.

It is not clear what effect the sanctions will have on the Legionaries movement. Defenders of Maciel argued he was the target of calumny because of his conservative theology. The Legionaries said Maciel accepted the Vatican's decision with "spirit of obedience to the Church."

"Facing the accusations made against him, he declared his innocence and, following the example of Jesus Christ, decided not to defend himself in any way."

Times staff writer Hector Tobar in Mexico City contributed to this report.