The train workers' union said in a statement that the strike, announced only late on Monday and starting at the morning rush hour, would run "indefinitely."
Two heavily used lines have been paralyzed by the action, which seeks to pressure the company into giving workers bonuses.
One line serves 370,000 passengers daily and has stopped functioning, while another serving 430,000 people a day has only partial service, the train company CPTM said.
CPTM called the strike "irresponsible" and asked workers "to be sensible and to provide the service on which 800,000 people depend each day."
The train workers' union was to meet later Tuesday to decide on what to do next.
Strikes and street protests are becoming increasingly common across Brazil as Latin America's biggest country struggles through its third straight year of recession, with unemployment at more than 13 percent.
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