It said there had been "an ignoble attempt to strike at Pope Benedict and his closest aides at any cost".
The editorial challenged a New York Times report about the case of Reverend Lawrence Murphy, accused of sexually abusing up to 200 deaf boys in the United States from the 1950s to the 1970s.
Among 25 internal church documents the newspaper posted on its website was a 1996 letter about Murphy to Cardinal Joseph Ratzinger, then the Vatican's top doctrinal official and now Pope Benedict, showing he had been informed of the case.
Ratzinger's deputy first advised a secret disciplinary trial but reversed that in 1998 after Murphy appealed directly to Ratzinger for clemency.
The priest died later that year.
The Vatican newspaper said: "There was no cover-up in the case of Father Murphy".
The Vatican said earlier he was not disciplined because church laws do not require automatic punishment.
The report came amid mounting allegations of sexual abuse by priests in Europe and pressure on bishops, mostly in Ireland, to resign for failing to report cases to civil authorities.
The pope apologisedon Saturday for decades of abuse in Ireland, but took no action against bishops blamed for cover-ups, which was met with disdain from numerous victims' rights groups.
Only 20 per cent of the 3,000 accused priests, whose cases went to the church's doctrinal office between 2001 and 2010, were given full church trials, and only some of those were defrocked, the New York Times reported.
Sixty per cent of those cases faced other "administrative and disciplinary provisions," such as being prohibited from celebrating mass, the newspaper said.
As the US abuse scandal has intensified in recent weeks, Pope Benedict chose not to say anything on Wednesday during his weekly public audience, an occasion when he offers greetings and messages in nine languages.
More than 300 former students in German Catholic schools and choirs have come forward since January with abuse claims. The country's government announced on Wednesday it will form an expert 40-member committee to investigate.
The allegations have come almost daily, including on Wednesday, when the Munich archdiocese confirmed that another person claimed to have been molested as a youth in 1998 by a priest who was previously convicted of abuse.
On Wednesday, Benedict XVI accepted the resignation of Bishop John Magee - an aide to three popes before assignment in Ireland - who has been accused of endangering children by failing to follow the Irish church's own rules on reporting suspected paedophile priests to police.