To the best of my knowledge, no Government organization will accept a duplicate certificate. All that you can do in the present circumstances is to get the police to certify that you have indeed lost your original certificate and that they are in the process of helping you to search it. Of course, you should have done this immediately, but given the circumstances, if you have by any chance not done so, then you can jolly well go the concerned police station and lodge a complaint. If you were with someone and that witness can testify to your having lost it, then the police record will become all the more strong.
In the meanwhile, the most prudent thing is to produce the police certificate and then request the University authorities to issue you a new Mark sheet. Legally, I am told that there is no hurdle at all. Hence, you need to check up with a local advocate and then request your concerned University authorities to issue you a new Marksheet.
If your Principal of the Degree College where you studied were to certify about your conduct and personal integrity, am told, the Railway Authorities will allow you to even join your job, on the specific condition that you need to produce the Original Marksheets within a specified time period. Please do note that the Railways may not insist on all mark sheets. For any further clarification, I suggest that you contact the local HR department of the Railway Zone under which your college is covered, to know the formal procedure. Once you get official guidance, you will be on the right path in getting your problem solved. The amount of flexibility in the rules is not known. However, you can check with the Railway authorities and do whatever is required.
Also, in the meanwhile, immediately lodge a police complaint and get the police to certify that you are being assisted in the process of searching for your original mark sheets and the degree certificate.