Members of the group Bekasi Muslim Friendship have objected to the construction of the Santa Clara church in Bekasi since a building permit was given to the Catholic Church in 2015.
Population: 263.5 million (31.9 million Christians)
Main Religion: Islam
Open Doors' World Watch List Rank: 46
Indonesia is the largest Muslim country in the world.
Mass protests against Governor Ahok of Jakarta, a Chinese Christian, for alleged blasphemy brought more than 200,000 people to the streets in 2016.
Bekasi Mayor Rachmat Effendi told local media that it was his top priority to ensure there was religious freedom in Bekasi and there was a public need for the building to be constructed.
He added that he would not be intimidated by the protesters and said: "No one can force or frighten me. I only follow the law."
Police officers were deployed to the site on Monday to discuss with church leaders how they can improve security.
At the protests on Friday, eyewitnesses told AP that the demonstrators tried to force their way into the property and threw rocks and bottles at the building. The police fired tear gas to disperse the crowds.
Local priest Fr Raymundus Sianipar was advised by police to leave the area for his own safety.
Approximately 12,000 Catholics live in Bekasi.
Indonesia is number 46 on Open Doors' World Watch List for Christian persecution.