Hundreds of people at Daru station in Jambe, Tangerang regency, protested on Monday against limitations on train passengers.
"We demand the government to review the policy because thousands of us were left stranded after its implementation," said Samsul, one of the protesting passengers.
The Transportation Ministry issued a ministerial decree in 2011 that limits the number of passengers to 150 percent of the train's capacity, to ensure safety.
The policy, however, was only recently applied at train stations.
Harry, another passenger at the station, said there were more than 500 people who took the same train every day but only 100 tickets were available on Monday.
"What will happen to us? It's difficult to get other public transportation without spending more money and time," he said.
Train operator KAI operational and supervision unit head Yuskal said the policy was implemented to provide comfort to passengers.
"It could be canceled if no more passengers climb on the roof and smoke onboard," he said.