Pope Francis has ordered a deeper investigation into the accusations of sexual misconduct against Archbishop Theodore E. McCarrick, the Vatican said Saturday, including a “thorough study” of archival documents to determine how he climbed the church hierarchy despite allegations he had slept with seminarians and young priests.

The statement came more than a month after Carlo Maria Viganò, the former Vatican ambassador to the United States, published a remarkable letter accusing the pope of having known about, and covered up, the actions of Archbishop McCarrick.

The Vatican statement did not explicitly address the accusations by Archbishop Viganò. Instead, the Vatican said, the pope’s decision was motivated generally by the “publication of the accusations” against Archbishop McCarrick, who once led the Archdiocese of Washington and was a major power in the Catholic Church in the United States.

The pope, the statement said, was “aware of and concerned by the confusion that these accusations are causing in the conscience of the faithful.”

Still, there is some resistance in the Vatican to taking concrete measures. Some bishops have said they consider abuse a problem that has been solved, a vestige from an earlier, less aware, era. Others believe it is drummed up by the secular news media, especially in the English-speaking world, to hurt the church.

Francis has become more aggressive this year in speaking out against abuse, accepting the resignations of Chilean bishops he once defended against accusations of covering up abuse. And he has argued that abuse, and its cover-up, are symptoms of “clericalism” — the notion that priests are more powerful than those they are supposed to serve.

On Saturday, the Vatican reiterated that it understood it needed to hold not only abusive priests accountable, but also the bishops who cover up for them.

“Both abuse and its cover-up can no longer be tolerated,” the statement said, adding that “a different treatment for bishops who have committed or covered up abuse, in fact represents a form of clericalism that is no longer acceptable.”

In July, Francis stripped Archbishop McCarrick of his rank of cardinal, prohibited him from exercising public ministry, and sentenced him to a life of prayer and penance. The steps came after “grave indications” were discovered in a preliminary investigation into the September 2017 accusation of a man who accused McCarrick of abuse in the 1970s, the statement said.

That investigation by the United States church found credible an allegation that Archbishop McCarrick, who referred to himself as “Uncle Ted,” groped the man as a teenage altar boy. Other accusations have followed, including by men who say they were abused as young teenagers.

The Vatican knew as early as 2000, during the papacy of John Paul II, about complaints from seminarians that Archbishop McCarrick was pressuring them to share his bed.

John Paul had moved Archbishop McCarrick, then in Newark, to the more prominent position of archbishop of Washington, prompting a professor at a New Jersey seminary to raise concerns in a November 2000 letter to the Vatican. John Paul, who allowed abuse to fester during his papacy, made Archbishop McCarrick a cardinal the following year.

In his letter, Archbishop Viganò asserted that Francis’s predecessor, Benedict XVI, who removed many abusive priests from the ministry, had punished Archbishop McCarrick. He accused Pope Francis in 2013 of ignoring or lifting the sanctions and rehabilitating the American as a political ally. There is still no evidence to support that allegation, and both Francis and Benedict have declined to comment.

Questions of who knew what and when have nevertheless consumed the Vatican since the publication of Archbishop Viganò’s letter in late August, as the pope visited Ireland, where the church has been devastated by abuse.

The Vatican said Saturday that it would dig into archives in the United States and the Holy See to “ascertain all the relevant facts, to place them in their historical context and to evaluate them objectively.”

Marie Collins, who was appointed to Francis’ first commission on child abuse and protection, said, “I wish those Vatican archives were opened up on all abusers. If they can open it up on McCarrick, open it up for everybody.”

Ms. Collins, an abuse survivor who quit the commission in frustration in 2017, added: “Survivors have been calling for that for years.”