The three victims died in the hospital today where they were undergoing treatment.
Around 132 others were also injured in the mishap that took place between Nagothane and Roha railway stations, over 100 kilometres from Mumbai.
Meanwhile, Maharashtra Chief Minister PrithvirajChavan is likely to visit the accident site and hospitals where the victims have been admitted for treatment.
The track, where the mishap took place, has been cleared and train traffic has been restored.
Preliminary examination has reportedly hinted at the possibility of a rail fracture as the cause behind the derailment.
While the government had ordered an enquiry into the incident, a compensation of Rs two lakhs was announced by the railways for those who have been killed.