The incident occurred on Thursday night when the youth, believed to be in his twenties, boarded the train at Grant Road station and molested her before she jumped off at a signal ahead of Marine Lines station.
"The victim, an MBA graduate, had boarded the compartment, which did not have a policeman guarding it, at Malad station," a GRP official said.
He said the accused youth boarded the train at Grant Road station, which is three station ahead of Churchgate.
The accused allegedly tore off her clothes. She screamed for help but her cries apparently went unheard, he said.
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After jumping off from the train at a signal before Marine Lines station, the victim went to the office of the station master at around 11:15 PM, who in turn took her to the railway police station at Churchgate.
"When the police started recording her statement, she consulted her friends and told them that she would visit next day as she was not feeling well," the official said.
"Since the matter is serious, the GRP decided to suo motu register a case of molestation and five teams have been formed to nab the accused," the official said.
Meanwhile, Deputy Commissioner of Police, Western Railway, has been asked to conduct an inquiry on the absence of policeman in the compartment and submit a report in a week.
There is a rule of deploying a policeman in women's coach after 11 PM.
"We will review our deployment process to detect any lapses. Efforts will also be made to make security (deployment) independent of any snags or delays (of trains) and more efficient irrespective of manpower constraints," the officer said.