Police have not made any arrests after Sunday's violence, when hundreds of stick-wielding Islamists stormed the peaceful rally in central Jakarta and severely beat dozens of people.
Victims of the attack joined with rights activists and the media on Tuesday in condemning the government for allowing a tiny minority of extremists to threaten basic rights in the world's most populous Muslim state.
The US embassy also urged the government to "continue to uphold freedom of religion for all its citizens as enshrined in the Indonesian constitution".
"This type of violent behaviour has serious repercussions for freedom of religion and association in Indonesia, and raises security concerns," the embassy said in a statement.
A little-known extremist group affiliated to the hardline Islamic Defenders Front (FPI) has claimed responsibility for the attack, saying they were "defending Islam".
The rally had been called to express support for constitutionally enshrined religious freedoms amid a debate over the minority Ahmadiyah Islamic sect, which the government is considering banning over its "deviant" beliefs.
FPI leaders held a press conference on Monday to announce they were preparing for war with Ahmadis and would fight "until our last drop of blood" to resist attempts to arrest them.
Many have questioned why the government is considering banning Ahmadiyah, which has peacefully practiced its faith in Indonesia since the 1920s, while doing nothing about violent religious vigilante groups.
President Susilo Bambang Yudhoyono has said the authors of Sunday's violence should be punished and has told ministers to examine options for banning the FPI.
But senior police officer Bambang Danuri said police were being careful not to provoke further violence and would wait for the suspects to turn themselves in.
"The president has condemned the actions of FPI, but there is no action in the field – it is only lip service," said Ahmad Suaedy, the director of a liberal Islamic think-tank who was badly beaten in Sunday's attack.
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.
But The Jakarta Post, an English-language daily, said in an editorial the country's freedoms were "in peril".
"We condemn the government that for the umpteenth time failed in its job to defend people in exercising their constitutional rights, first with regard to freedom of religion and now freedom of expression," it said.
"The latest threat comes not so much from those who want to take our freedoms away, as from the failure of the state to protect us from exercising our rights."
Several observers noted that the FPI was used by the Suharto dictatorship to intimidate pro-democracy activists in the 1990s and retains close contacts with elements of the security forces.
The police were also said to be treading carefully after weeks of almost daily protests against rising inflation and a 30-per-cent hike in the price of subsidised fuel last month.
"The police could have acted quickly, but they also have to take into account the political tug of war. Otherwise the results could be further conflict," criminologist Adrianus Meliala said.