Some 100 Christian worshippers intended to hold a mass near empty land where they hope to build a church, about 30-kilometre east of the capital, in a project barred by district government and community members in 2009.
Since then, worshippers from the Filadelfia Batak Christian Protestant have held Sunday services under scorching sun outside the property.
On Tuesday, however, local community members blocked the road near the land, Andri Ananta, a local police chief on Jakarta's outskirts, told AFP.
An AFP photographer witnessed furious locals - men and women, with small children in tow - physically blocking the road and throwing rotten eggs at the gathering worshippers.
Ananta said police managed to convince the Christians to drop their plan and return home.
"We tried our best to avoid any clash and the Christians agreed to leave," he said, adding 380 police and military personnel including an anti-riot squad were deployed to the area.
Church leader Reverend Palti Panjaitan said the incident came after a Christmas Eve attack Monday evening when "intolerant people" threw not only rotten eggs but plastic bags filled with urine and cow dung at them.
"Everything had happened while police were there. They were just watching without doing anything to stop them from harming us," he told AFP.
The country's high court last year overruled the district government's 2009 decision, but constant intimidation from Muslims in the area has delayed the church's construction, church officials said.
Indonesia's constitution guarantees freedom of religion but rights groups say violence against minorities including Christians and the Ahmadis has escalated since 2008.
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Surely religion is a dangerous tool in the hands of idiots.
They are getting infected by Wahhabi thinking which is not reflective of the religion's spirit. But Muslims governments do not have gut to tell off the Saudis for trying to spread their malign beliefs using petrodollars.