Archbishop Angelo Bagnasco, who is president of the Italian Bishops Conference and also the archbishop of Genoa, said it would be ''inopportune'' to use the prayer, a popular devotion among Catholics, during a political demonstration.
The proposal to build the mosque has divided residents of the port city, with some saying that its growing Muslim community had a right to a place of prayer and others saying it would be offensive because it is near a church.
The demonstration against the mosque has been organised for tonight by the local branch of Forza Italia, the conservative party whose national leader is former prime minister Silvio Berlusconi.
The protesters plan to pray the rosary, which consists of the ''Our Father'', ''Hail Mary'' and ''Glory Be'' prayers, while they march from a city square to the site of the proposed mosque.
Some of those who planned to participate rejected Bagnasco's call, saying he could not tell them when and where to pray.
Tensions between local communities in predominantly Catholic Italy over new mosques to serve the growing number of Muslims flare up regularly.
In December 2006, protesters left a severed pig's head outside a mosque being built in the Tuscan town of Colle di Val d'Elsa. In July, police arrested an imam in central Italy on suspicion of leading a terrorism ''training school'' in a mosque in Perugia.
After that arrest, Italy's anti-immigration Northern League called for all existing mosques, most in old garages or converted factories and warehouses, to be closed for security checks.
Italy's largest mosque is in Rome and was built in 1995 with the blessing of the Vatican.
Reuters SG GC1602