Dressed as Christian pilgrims, the trio entered the Roman Catholic Basilica of the Annunciation in Nazareth, pushing a child's pram filled with fireworks and small gas canisters, reported Agence France-Presse (AFP).
They were overpowered by angry worshippers and the man was injured. No damage wad done to the ancient church.
After several hours of mayhem inside and rioting outside, police managed to evacuate the man, his wife and daughter safely from the church.
Internal Security Minister Gideon Ezra, who happened to be in the Israeli Arab town, confirmed that "two women and a man threw something that made a huge noise in the church. The police subsequently defended them from the crowd inside the church. We called in urgent reinforcements."
The man was identified as Haim Eliahu Habibi, a Jew from west Jerusalem. The Habibis are known to police and security services as having a history of threatening to attack churches, according to Israeli television reports.
Protesters gather at the gate of the church. (Reuters)
Security forces fired tear gas to disperse the angry worshippers. Around a dozen police were injured in clashes and a police car was set on fire.
Police dispatched anti-riot and anti-terrorist units to the church. Local television showed them using batons and stun grenades to keep protesters back.
Israeli officials sought to quickly defuse anger and said security at churches and mosques would be stepped up, Reuters reported.
Arab community leaders will meet on Saturday, March 4, before joining a planned protest march in the town's streets.
Israeli Foreign Minister Tzipi Livni spoke to her Vatican counterpart to explain the situation and to say it was under control, a ministry official said.
Ezra said this was a "provocation whose motives we do not know for now."
"I hope that with the help of city and church officials we can bring this matter to an end without further incident," he added.
Nazareth, which has a sizable Christian community, is the largest Arab town in modern-day Israel. Thousands of its indigenous people were forced to flee their homeland by Zionist gangs, who established the state of Israel on the rubble of Palestine in 1948.
It is believed that it was in Nazareth that the Archangel Gabriel appeared to the Virgin Mary and announced to her that she was to conceive and bear a son, who was to be called Jesus.
The basilica is the largest in the Middle East. The modern structure was consecrated in 1969.Last Mod: 20 Eylül 2018, 18:16