The incident came to light yesterday, when the victim was found severely injured in Kotwali area, they said.
"The girl was found seriously injured and profusely bleeding near Bhakt Kanwarram Market near Kotwali police station after which she was admitted to the Chhattisgarh Institute of Medical Sciences (CIMS) hospital last morning," Bilaspur Superintendent of Police Ratanlal Dangi told PTI.
The victim's medical examination has confirmed rape, he added.
The girl was travelling on the Howrah-Kurla Express and when she went to relieve herself yesterday an unidentified man allegedly followed her there and raped her, the victim said in her complaint.
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"Although the police have not been able to record her statement because of her severe injuries, she narrated the incident to the Kotwali police as she was being taken to hospital," the SP added.
"She was unable to tell how she managed to reach the city from Bilaspur railway station," he said.
A case has been registered against an unknown person, while efforts are on to ascertain his identity, he said.
Meanwhile, the railway police has announced a cash reward of Rs 25,000 for information on the accused and are investigating closed circuit television camera footage from the railway station.