The Italian Bishops Conference said Benedict had spoken by telephone with its president, Cardinal Angelo Bagnasco, to discuss the "current situation."
Benedict expressed to Bagnasco "his esteem, gratitude and appreciation," the Bishops Conference said in a statement. Vatican officials confirmed the phone call but would not elaborate.
Bagnasco and other top church officials have been defending a Catholic editor who was attacked by a Berlusconi family newspaper after demanding that the premier answer allegations over his purported relationships with young women.
Il Giornale, which is owned by the premier's brother Paolo, on Friday alleged that the chief editor of the Avvenire daily had a homosexual scandal in his past.
The paper alleged that Dino Boffo had been fined several years ago for harassing the wife of a man in whom he was purportedly interested. Boffo has denied the allegations.
The Bishops Conference, which owns Avvenire, staunchly defended Boffo, and Bagnasco called the allegations "disgusting."
Berlusconi quickly distanced himself from Il Giornale's claim, but the incident damaged the premier's church ties, already frayed by the scandal.
Following Il Giornale's article, a meeting between Berlusconi and the pope's top aide, Cardinal Tarcisio Bertone, was scrapped. The meeting had been widely seen as a chance for Berlusconi to clear the air with the Vatican.
Support from Catholic voters is considered crucial for any Italian government to come to power, and good ties with the Vatican are courted by many politicians.
Berlusconi has been on the defensive since his wife announced in spring she wanted to divorce the premier, citing his alleged relationships with young women. Allegations have included that women were paid to attend Berlusconi's parties, while a high-class prostitute said she spent a night with him at his Rome residence.
Berlusconi has denied having any improper relationships or paying women for sex, and dismisses the scandal as a plot by left-leaning media.
But many, including Avvenire, have demanded more answers from the 72-year-old conservative billionaire media mogul.
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SIC: AP