CHICAGO — Prosecutors in Minnesota filed criminal charges on Friday against the Roman Catholic Archdiocese of St. Paul and Minneapolis, accusing church leaders of mishandling repeated complaints of sexual misconduct against a priest and failing to follow through on pledges to protect children and root out pedophile clergymen.

The charges and accompanying civil petition, announced by the Ramsey County prosecutor, John J. Choi, stem from accusations by three male victims who say that from 2008 to 2010, when they were under age, a local priest, Curtis Wehmeyer, gave them alcohol and drugs before sexually assaulting them.

The criminal case amounts to a sweeping condemnation of the archdiocese and how its leaders have handled the abuse allegations — even after reforms were put in place by church leaders to increase accountability — and the charges are among the most severe actions taken by American authorities against a Catholic diocese.

“Today, we are alleging a disturbing institutional and systemic pattern of behavior committed by the highest levels of leadership of the Archdiocese of St. Paul and Minneapolis over the course of decades,” Mr. Choi said in a statement.