Protesters covered their faces and scattered in all directions as chaos erupted in the centre of the sprawling capital, Jakarta.
Police also fired tear gas at rock-throwing protesters in Makassar on Sulawesi island, while demonstrators broke down a barrier outside the governor's office in Semarang on Java island.
"(We) forcibly dispersed student because they were carrying out anarchist acts, damaging government property and throwing stones at police," said Dicky Sondani, a South Sulawesi police spokesperson.
The police action came after flag- and placard-waving demonstrators gathered across the Southeast Asian archipelago -- including in cultural capital Yogyakarta and holiday hotspot Bali -- for a second day in a row.
On Tuesday, lawmakers debated a wide-ranging legal overhaul including hundreds of new laws that would criminalise pre-marital sex, restrict sales of contraceptives, make it illegal to insult the president, and toughen the Muslim majority country's blasphemy laws.
A vote on the bill was originally scheduled for Tuesday, but President Joko Widodo last week called for a delay in passing the proposed changes after a public backlash.
Couples flogged for public affection in Indonesia province
The mooted changes could affect millions of Indonesians, including gay and heterosexual couples who might face jail for having sex outside wedlock, or having an affair.
Widodo's call for a delay came as the Australian embassy in Jakarta issued a fresh travel advisory, warning that the legislation could put unmarried foreign tourists in the cross hairs.
Millions of tourists visit Bali and other beach destinations in the Southeast Asian nation.
Widodo this week stood firm on plans to pass a separate bill that critics fear would dilute the investigative powers of the corruption-fighting agency -- known as the KPK -- including its ability to wire-tap suspects.
Updating Indonesia's criminal code, which dates back to the Dutch colonial era, has been debated for decades and appeared set to pass in 2018 before momentum fizzled out.
A renewed push this year, backed by conservative Islamic groups, was met with a wave of criticism over what many saw as a draconian law that invaded the bedrooms of a nation with some 260 million people -- the fourth most populous on Earth.
An online petition calling for the bill to be scrapped garnered half a million signatures, while hundreds of thousands took to social media to vent their frustration.
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