This week's report from the Attorney General alleged Bishop James Timlin covered up allegations of abuse against priests and authorized payments to victims.
"The abuses described in the report are criminal and morally reprehensible", Greg Burke, the Vatican spokesman, said in a statement.
The statement stressed the "need to comply" with civil law, including mandatory reporting of abuse against minors and said Pope Francis understands how "these crimes can shake the faith and spirit of believers" and that he wanted to "root out this tragic horror".
Earlier on Thursday, U.S. Roman Catholic bishops called for a Vatican-led probe backed by lay investigators into allegations of sexual abuse by former Washington Cardinal Theodore McCarrick, who resigned last month. The Pope himself has yet to comment on the accusations in the almost 900-page report.
In numerous dioceses that have been examined, the numbers have been staggering: in the six Pennsylvania dioceses, 300 abusive priests and more than 1,000 victims since the 1940s; in Boston, at least 250 priests and more than 500 victims.
"There are so many things the church speaks about that are politically sensitive topics", said Kurt Martens, a professor of canon law at The Catholic University of America.
The U.S. Conference of Catholic Bishops said it was "shamed and sorry for the sins and omissions by Catholic priests and Catholic bishops" but that reforms such as the Committee for the Protection of Children and Young People and the office of the Secretariat of Child and Youth Protection "offer avenues to healing for those who have been abused".
"The Church must learn hard lessons from its past, and there should be accountability for both abusers and those who permitted abuse to occur", Burke said.
In his statement, Burke noted that nearly all of the abuse discussed in the report happened decades ago, and very few cases have been presented since the sex abuse crisis of 2002.
In recent years, the US bishops have adopted widespread reforms, including mandatory criminal background checks for priests and lay employees, a requirement that abuse allegations be reported to law enforcement, the suspension of priests while they are being investigated, and permanent removal from ministry when accusations are substantiated.
While Burke called for "accountability", there is little agreement among Catholic leaders about what that might mean.
The grand jury's roughly 900-page report released Tuesday is now seen as the most exhaustive investigation of the sexual abuse of children in the Catholic Church by any state.
The so-called Dallas Charter - approved by US Catholic bishops in 2002, after sex abuse was first unearthed in Boston - implemented discipline for abusive priests, but did not extend all the way up to bishops.
"The clock is ticking for all of us in Church leadership", CNN quoted Cardinal Sean O'Malley of Boston, the Pope's top adviser on sexual abuse, as saying on Thursday. It contained graphic examples of children being groomed and sexually abused by priests. "We firmly resolve, with the help of God's grace, never to repeat it".