One of the people who died on the train has not been identified yet.
Two people were found dead when a train from Mumbai arrived in Varanasi on Wednesday amid a push to return migrant workers home after weeks of a gruelling nationwide COVID-19 lockdown that left lakhs without income, food and shelter.
The Shramik (Workers) Special train arrived in the Uttar Pradesh city's Manduadih station two days after leaving from Mumbai. It had around 1,500 passengers on board.
"The train came from Mumbai's Lokmanya Tilak station at 8:20 in the morning. After all the passengers got off, we learnt that two people had been found dead. The GRP (Government Railway Police) is trying to find out more details," Arun Kumar, the Station Master, told NDTV.
One of those found dead included a person with disabilities who, authorities said, had been unwell.
"The family told us he had not been keeping well for many days," a police officer said.
The other person, found in a different coach, has not yet been identified. He was travelling alone.
The police have sent his body for an autopsy.
Lakhs of migrant workers and their families were left to fend for themselves after India went into a sudden shutdown in late March - two months after the coronavirus pandemic hit the country.
Without jobs or access to food, the migrants set out for their homes thousands of kilometres away, walking or taking cycles and trucks. Dozens have fallen sick or died on their journeys, either from fatigue or in accidents.
After over six weeks of horrific scenes of pregnant women and exhausted children trying to reach home, the government started special trains to take migrants home, but the process has been vexed by paperwork and glitches, which led to many still making their own desperate arrangements to go home.
In the soaring heat, migrant families have been forced to wait in queues, either for tickets or at centres where they are screened and declared virus-free to travel on trains.
Temperatures have touched 50 degrees in parts of India, adding to the suffering of labourers and families on the move.