More than 100 activists from the Islamic Defender Front staged a peaceful protest as about 200 riot police and two water cannon stood guard.
The protesters carried banners saying, "Holland go to hell" and "Kill Geert Wilders," the film's maker.
By repeatedly saying "Allahu Akbar!" or "God is Great!", the protestors pelted the embassy with rotten eggs, witnesses said.
Last Mod: 31 Mart 2008, 14:34
"We urge the Indonesian government to cut off its diplomatic relations with the Netherlands because the Dutch government had failed to stop the film," one protestor shouted.
After about an hour, the demonstrators dispersed with no arrests reported.
Wilders, an anti-immigration politician, released the film over the internet late Thursday after publicizing its release for months.
Indonesia's Foreign Ministry described the film as "misleading and full of racism" and called the production of the film an "irresponsible action done under the blanket of freedom of expression."
Cleric Abu Bakar Ba'asyir urged the Indonesian government to take stronger measures against the Dutch, including boycotting all Dutch products and cutting off diplomatic ties.
A number of Indonesian lawmakers also called for boycotts of Dutch goods along with travel warnings for Indonesians visiting the Netherlands.
Since the film's release, Muslim leaders and Indonesian politicians have condemned it, saying it was misleading and would hurt interfaith dialogue.
At another demonstration Sunday, hundreds of junior high school students in the Central Java city of Magelang demanded authorities shut down websites carrying Wilders' film.
Indonesia is the largest Muslim nation with nearly 88 per cent of its 225 million people adhering to Islam.