The students at the Institute of Islamic Studies have reportedly refused to move and have been joined by residents in the area.
At least two protestors were injured when the police fired warning bullets and tear gas in an attempt to disperse angry students who ignored orders to stop burning tyres outside a university in south Jakarta.
The students at the Institute of Islamic Studies have reportedly refused to move and have been joined by residents in the area.
The government announced the 30% price rise on Friday, abandoning heavy subsidies in a desperate bid to reduce its huge budget deficit.
The measure has prompted bus drivers in six cities to go on strike, Reuters news agency said, leaving thousands of commuters stranded.
Scuffles
Police and protesting students also scuffled in front of the Indonesian Christian University in East Jakarta, AFP news agency reported, after students began to throw objects at police.
And in the centre of the city, furious students burned tyres and scrap wood in front of the University of Indonesia.
Raising fuel prices is always politically risky in Indonesia - it helped bring about the downfall of former President Suharto in 1998.
The police have reportedly put 42,000 personnel on high alert in the capital to avert further violence and to guard against a transport strike there. So far the bus drivers' action has only affected cities outside Jakarta.
"If strikes go ahead and protests turn into anarchy we will take all necessary steps," police spokesman Brigadier-General Didi Widayadi told Reuters.
Drivers argue that there should be a raise in prices to accompany the increase in fuel cost. The authorities in one central Javan city have already given into their demand.
Stranded
The strikes have forced the Indonesian authorities to provide army and police trucks to transport stranded passengers.
Most of the population in the world's largest archipelago depends on public transport.
The cities affected are the oil port city of Pekanbaru in Riau province on Sumatra island, the eastern city of Sumbawa Besar in Nusa Tenggara, and at least four cities in eastern Sulawesi island, Reuters said.
Even where strikes were not taking place customers were being hit by the unrest.
"After a hot debate with the driver, I had to pay more than usual. He said that fuel was already up so the fare also must go up," commuter Yos Piliang told Reuters in the industrial city of Medan on Sumatra island.
The angry public reaction to the fuel rise is likely to put further pressure on Indonesian President Abudrrahman Waid who is facing an impeachment hearing in August.