"The cubs were hit by a train early on Thursday and their mangled remains were recovered and sent for post-mortem," A.K. Mishra from Maharashtra state's forestry department told AFP.
Their bodies were spotted in Maharashtra's Chandrapur district, which is famous for a thriving tiger population.
"The incident is extremely unusual and we have not spotted their mother yet and will cremate them soon," Mishra said.
India has launched a major campaign to boost tiger numbers. At the last tiger census in 2014 the population had risen to more than 2,200 from a low of less than 1,500.
But as urban areas have expanded in the country of 1.25 billion people, conflict between humans and tigers has worsened. Poaching is also a concern.
A controversy is meanwhile raging about the death in early November of a tiger believed to have killed more than a dozen villagers, also in Maharashtra.
The tigress was shot after a months-long search using paragliders, infrared cameras, sharpshooters on elephants and even Calvin Klein perfume.
The big cat was shot dead by Asghar Ali Khan, the son of India's most famous hunter Nawab Shafath Ali Khan, in seemingly murky circumstances.
Foresty workers were on Thursday looking for the tigress's two cubs, with Mishra saying they had been spotted in a forest and was hopeful they would be found.
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