The priest, who has not been named, banned the prayer during a mass held at the weekend in a small church in Passo San Boldo, near Treviso.
The region is a stronghold of the famous Alpini, Italy's elite mountain army corps established in 1872, and the ‘Prayer of the Alpino' was written by a soldier to his mother in 1935 and later adopted by the troops.
The priest reportedly told the faithful that since there were crowds of desperate immigrants pushing to enter Italy's borders it was inappropriate to speak of a call to arms.
The conflict also provoked an outburst from Matteo Salvini, leader of the anti-immigrant Northern League, who supported the Alpini on his Facebook page.
“I am more and more baffled by ‘certain bishops',” Salvini said.
The cleric's controversial move was backed by the local Catholic diocese of Vittorio Veneto. But those loyal to the Alpini walked out in protest and recited its full text outside the tiny church, Italian media reported.
Angelo Biz, president of the local branch of the National Alpini Association (Ana), said he wanted to avoid any conflict but said he wondered why “the relationship between the diocese and the Alpini often became so problematic.”
Since the 1990s he said the version of the prayer adopted by Ana in 1949 was read out whenever events were held with members.
“Only a hypocrite or an ideological pacifist would think that the Alpini support sentiments of aggression and intolerance,” he told the daily, La Nazione.
The Alpini are considered the oldest active mountain army corps in the world. Their original mission was to protect the mountainous border region with France and Austria and the troops fought a critical three-year campaign against the Austrians and the Germans during World War One. They also fought in World War Two and soldiers from the Alpini are currently deployed in Afghanistan.