BOSTON — Cardinal Seán O’Malley of Boston responded swiftly to accusations by two former seminarians of sexual misconduct and other immoral behavior at St. John’s Seminary, placing the rector on sabbatical leave and launching a formal investigation.

The investigation comes in the context of the nationwide Catholic examination of conscience over sexual abuse triggered by a number of recent scandalous revelations regarding past and current sexual abuse by Catholic clergy. It has focused attention to the state of St. John’s Seminary in nearby Brighton, in terms both of the current situation of the seminary as well as of measures that were undertaken in recent years to address problems that came to light in the wake of the 2002 U.S. clergy-abuse scandal that was centered in Boston.

The move came after former seminarian John Monaco published an article on OnePeterFive.com in early August alleging homosexual behavior among some seminarians and excessive drinking at parties, including one incident in which a faculty member was so intoxicated that he fell out of his chair. Monaco also recalled similar incidents at a second seminary in Pennsylvania.

His account of the seminary was corroborated by comments from another former seminarian on the archdiocesan Facebook page.

On Aug. 10, Cardinal O’Malley announced that seminary rector Msgr. James Moroney would be on sabbatical for the fall. He appointed Father Stephen Salocks, a Scripture scholar at the seminary, the interim rector.

Cardinal O’Malley is also conducting a probe into the “culture of the seminary” and “any issues of sexual harassment or other forms of intimidation or discrimination.” In order to focus on the matter, the cardinal canceled his trip to the World Meeting of Families in Ireland in August.

Terrence Donilon, the secretary for communications and public affairs for the Archdiocese of Boston, declined to comment to the Register on any aspects of the investigation. He said the rector’s departure was a mutual decision aimed “in order to guarantee the independence of the process and in order to foster an environment of complete freedom where information is shared without reservation.”

One source who is familiar with archdiocesan operations suggested that Msgr. Moroney’s departure is not a surprise. He said Msgr. Moroney, who assumed his post in 2012, has been criticized for being more focused on external seminary affairs, like fundraising and growing the student body, and has been less of a hands-on presence on campus. The rector has also come under fire over his fiscal management at the seminary.

The seminary is also facing declining enrollment as other New England dioceses refer their seminarians elsewhere, fueling fears that there might be deeper problems at the seminary, according to the source, who would speak only under condition of anonymity.

He noted that Father Salocks has no previous experience in the administration of the seminary but has a reputation as a holy priest. It’s a sign, according to the source, that Cardinal O’Malley wanted someone who was not part of any potential problems at the seminary.

“Clearly Cardinal Sean wants to make a statement that the seminary is going to form holy priests,” the source said.

The normally more deliberative Cardinal O’Malley’s speedy response came as a “shock” to most people, but his action is also consistent with his approach to the aftermath of the sex-abuse crisis, which broke in 2002, according to the source. Cardinal O’Malley was appointed after his predecessor, Cardinal Bernard Law, resigned.

Cardinal O’Malley, who was named a cardinal in 2006, currently serves on an eight-member commission of cardinals responsible for Church administrative reforms in the wake of the recent sex-abuse scandals. He is also the president of the Pontifical Commission for the Protection of Minors and has earned a reputation for toughness and transparency on the issue.

Soon after the seminary story broke, Cardinal O’Malley also faced news that he had not responded to a 2015 letter from a priest warning about misconduct by former Cardinal Theodore McCarrick, who was removed from the College of Cardinals this summer after abuse allegations surfaced.

Cardinal O’Malley apologized for the oversight. “Allegations regarding Archbishop McCarrick’s sexual crimes were unknown to me until the recent media reports. I understand not everyone will accept this answer, given the way the Church has eroded the trust of our people. My hope is that we can repair the trust and faith of all Catholics and the wider community by virtue of our actions and accountability in how we respond to this crisis,” he said in an Aug. 20 statement.

After Cardinal O’Malley intervened in the seminary, Monaco followed up with a second article, detailing his accusations and warning of a “toxic culture of fear, intimidation and discrimination” and alleging “cover-up of such misconduct and unhealthy culture by leadership.” One former seminarian at St. John’s, who is now a priest in Massachusetts, said that the parties described by Monaco did happen “on occasion” — including the incident involving one inebriated faculty member, who has a reputation for hosting the raucous parties. But he also said that only a small number of students participated.

“Drinking is a huge problem,” said another former seminarian who also would only speak on condition of anonymity. He said it wasn’t only the faculty member’s parties. He said seminarians would often drink heavily in the common area on Thursday evenings, berating those who declined to participate as lacking in fraternal charity. But he said the issue was not so much the culture of the seminary as individual men who didn’t understand what it meant to be “married to the Church” and instead lived more like bachelors.

Both former seminarians told the Register the school’s leadership tended not to take action on reports of misconduct unless they were provided with overwhelming evidence. Both men said St. John’s problems aren’t necessarily systemic; both referred to seminarians’ experience there as a “mixed bag.”

“St. John’s, from what I know, is one of the better seminaries,” one added. St. John’s, despite the extent of its current problems, has already undergone some reform and renewal. That was spearheaded by Dominican Father John Ferran, now retired, who served as rector of the seminary from 2003 to 2007.

Upon arriving, he said he had to undertake a number of reforms — and not just because of the sex-abuse crisis that rattled the archdiocese in his first year. One issue he faced was a disproportionately high number of faculty members relative to students. “So change had to take place,” Father Farren said in an interview with the Register in August.

In his first year, he focused on improving the courses at the seminary and solidifying their doctrinal content. Amid the overhaul, the seminary saw the departures of many faculty members.

One major change was cultural. Father Farren said that he instituted a daily Holy Hour for seminarians — over the objections of some faculty members who claimed such routine prayers would not prepare them for the disorderly and unpredictable life of being a parish priest.

Father Farren said the Holy Hours contributed to a “sea change” in the culture of the seminary. “At the end of that first year … you had a sense this is a place where people pray, where they talk to God. It was palpable,” Father Farren said. “That was not the case when I first got in there. That first year was a year of marvelous change.”

Father Farren — who is not involved in any way in the current investigation — was also in charge of implementing several Vatican initiatives on seminary life. One was the 2005 guidance from the Congregation of Catholic Education aimed at barring active homosexuals and those with deep-seated homosexual tendencies from being admitted to seminaries.

The retired priest said he did not have to change the seminary’s admissions policies because it was already in compliance with the instructions. He said a later visit from a USCCB committee of lay investigators appointed to monitor the response among U.S. seminaries reached the same conclusion.

During his time as rector he did dismiss two seminarians for homosexual conduct, but he said he did not have to deal with the kind of partying behavior alleged to have occurred at the seminary more recently.

“The fact that that happened is not to me terribly surprising,” Father Farren said. “It’s disappointing in the sense that the screening of candidates prior to entering into the seminary is done as well as it can be done.”

Stephen Beale writes from Providence, Rhode Island.