At least a dozen people were injured, including three who required hospital treatment after being attacked, reportedly by FPI supporters wielding bamboo sticks.
The march took place amid an ongoing debate over whether a minority group, the Ahmadiyah sect, should be banned for what critics say is its "deviant" interpretation of Islam.
The attack on Sunday's rally has drawn widespread condemnation, including from Indonesia's largest Islamic organisation, the Nahdhatul Ulama, which claims some 40 million members.
Yenni Wahid, director of the Jakarta-based Wahid Institute, told Al Jazeera that it was up to the Indonesian security forces to take decisive action.
"We are ready to fight a war against Ahmadiyah with all our followers whenever, wherever"
Habib Riziek Syihab,
"As long as the security forces are still acting as they do now, it won't change anything," she said.
"The key thing is the government, the government needs to make sure that stern measures that groups like that are not tolerated in Indonesia, whatever names they take up."
The attack also drew a warning from the US embassy which issued a statement on Tuesday condemning the violence.
"This type of violent behaviour has serious repercussions for freedom of religion and association in Indonesia," it said.
But on Tuesday Habib Riziek Syihab, the leader of the FPI, was unrepentant telling his supporters to prepare for war.
"We are ready to fight a war against Ahmadiyah with all our followers whenever, wherever," he said.
"We will not accept Islam to be defiled by anyone. I prefer to be in prison or even be killed than accepting Islam to be defiled."
Susilo Bambang Yudhoyono, Indonesia's president, has called for those behind Sunday's violence to be punished, but so far the police have taken no action against the group.
Late on Monday Yodhoyono told ministers to examine options for banning the FPI under a 1985 law that allows for the dissolution of groups that "disturb public security and peace."
With some 230 million people, Indonesia is the most populous Muslim state and has a long history of religious pluralism and tolerance which is guaranteed under the constitution.