The protesters, who were organized by the hard-line Islamic Defenders Front (FPI), marched from a mosque to the company's headquarters, which was shielded by hundreds of police. Many carried signs that read 'Don't persecute Muslims' and 'Please don't judge our status on Facebook.'
FPI spokesman Slamet Maarif said the protesters want to know why Facebook blocked the accounts while allowing others that denounced its leaders and Islam to continue to operate.
'We want justice and no more discrimination against Islamic accounts,' Maarif said.
Facebook spokeswoman Putri Ariani said the company allows account holders to use the network to express opposing views and raise awareness, but deletes content that encourages hatred and violence.
FPI wants to impose Shariah law in Indonesia, the world's largest Muslim-majority country that is overseen by a secular government.
The southeast Asian country has a reputation as a tolerant and diverse society that respects freedom of expression. Most Indonesians adhere to a moderate form of Islam, but a small extremist segment of the population has become more outspoken in recent years.