The attack, during which stones and dirt were also hurled, occurred on Thursday as around 100 Christians prepared to hold a service at a church in Bekasi, a city on the outskirts of the capital Jakarta.
Members of the Philadelphia Batak Christian Protestant Church have been targeted several times in recent years.
"They attacked when the priest started to speak to the congregation. A crowd of 600 people threw bags of urine and dirty water as they tried to push police," a lawyer for the church, Judianto Simanjuntak, told AFP.
"Police didn't even try to disperse the crowd, so they were open to attack us."
National police spokesman Saud Usman Nasution confirmed there was an incident and that "an investigation has started, although no one has been arrested".
In 2009, the local administration ordered the church be shut down, but a provincial court overruled the decision, which was also upheld by the Supreme Court last year.
Several other churches in Bekasi have suffered attacks in recent years, the worst leaving a priest badly bashed and an elderly leader stabbed during a Sunday service in 2010.
Simanjuntak said that groups of hardliners had intimidated Christians in Bekasi several times this month and that leaders of the Islamic Defenders Front (FPI) had been spotted among them.
There has been more criticism this week that hardliners are wielding too much power in the country after the police Tuesday refused US pop singer Lady Gaga a permit to perform in Jakarta.
The FPI, which has carried out mob attacks in recent years on Islamic minority groups and Christians, promised chaos if the provocative performer entered the country.
Police also shut down several events held by Canadian writer Irshad Manji after the FPI held violent protests condemning Manji's liberal views on Islam as well as her homosexuality.
Ninety percent of Indonesia's population of 240 million identify themselves as Muslim.
COMMENTS (7)
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ
After loosing a part of country to the Christian converts with Western support, poor Indonesians are too skeptical of such events. But the way to peaceful coexistence is education, tolerance and compromise not violence & retaliation.
I guess we know why Indonesia is the only country that seems to admire Pakistan -- fellow xenophobic country that likes to pick on minorities.
This is NOT the Islam that the Prophet (PBUH) strived for. Places of worship are given utmost respect.
I have watched a bbc documentary on this issue and it seems a long dispute. . It seems the church is an illegal one and congregation is against the local laws. . Despite all this, no excuse for such actions! This is horrible thing to do to anyone, let alone minorities! Only administration has a right to take action.
That is sick
Indonesia on its way to become next Talibanistan. I won't be surprised if US fires few drone missiles there in the future.
Indonesia on it's way to become next Talbanistan. I won't be surprised if US fires a few drone missiles there in future.