ROME—A senior Vatican official on Sunday denounced what he called the “monstrous accusation” that Pope Francis ignored reports of sexual misconduct by a favorite U.S. cardinal, but he also confirmed that the cardinal had already been under disciplinary measures when the pope took office.

Cardinal Marc Ouellet, head of the Vatican’s office for bishops, called claims that the pope knew of allegations against then-Cardinal Theodore McCarrick yet made him an important adviser in the U.S. church “calumny and defamation.”

He acknowledged, however, that when the pope took office in 2013 the cardinal had already been punished over widespread rumors he had been sexually active with seminarians. That is a key element in the argument that the pope must have known about his past.

An investigation later found credible evidence that the then-cardinal had sexually abused a teenager in the early 1970s, and in July he became the first man to give up the title of cardinal in nearly a century.

The accusations by Archbishop Carlo Maria Viganò in August have rocked the church and shaken faith in the pontiff’s credibility.