Thousands of Christians have held a protest rally in the Galilee, near the historic church in northern Israel that was seriously damaged after a suspected arson attack which included anti-Christian sentiment scrawled in Hebrew on a wall.

The Church of the Multiplication in Tabgha was set on fire early on June 17 and the suspected hate crime drew fierce condemnation from Israeli leaders from major political parties, The Times of Israel reported.

Inside the church former Latin Patriarch of Jerusalem Michel Sabbah and Bishop Giacinto-Boulos Marcuzzo, auxiliary of the Latin Patriarchate, celebrated a Sunday Mass attended by hundreds of young people on June 18.

Many carried crosses and waved Vatican flags and Jewish, Muslim and Druze clerics came the church to express support, The Catholic Herald reported.

The church is run by the Catholic Benedictine Order and is known for its fifth-century mosaics, including one depicting two fish flanking a basket of loaves.

"The attack on the church is an attack on all those who believe in a civilization of love and coexistence," said Father Gregory Collins, the head of the Order of Saint Benedict in Israel, to protestors.

In an entrance corridor of the building, believed by Christians to be the site of Jesus's miracle described in the Bible of multiplying two fish and five loaves to feed 5,000 people, Hebrew graffiti was found.

It read, "The false gods will be eliminated," The Times of Israel reported saying it is a quote from Jewish liturgy.

Prime Minister Benjamin Netanyahu said he had instructed the Shin Bet security agency to swiftly apprehend the perpetrators, but no suspects had been immediately arrested.

"This despicable act is trying to damage the fabric of society in the Galilee," said Daria Arbel, one of the demonstrators and a member of the interfaith organization Marching Together to a Shared Future.

"We live here together, people of all religions, and we won't let anyone damage this shared life we have here."

Shadi Halul, the chairman of the Aramaic Christian Association in Israel, also condemned the "abominable act, just like any damage to a Jewish holy place would be."

"We have a shared past and a shared future as well. Those that did this do not represent the Jews and actually hurt the Jews.

"They undermine the Jews' right to exist here and achieve the opposite result because haters of Israel take advantage of this and use it against the Jews," Halul said.

An adviser to the Catholic Church blamed Jewish extremists for the incident, which has been widely condemned by religious and secular authorities in Israel.