Millions of daily-wage earners were stranded with no means of income after India went into lockdown on 24 March to curb the spread of coronavirus.
Some tickets can cost around 800 rupees ($11;£9). A daily-wage earner typically makes between 200 and 600 rupees a day.
India’s main opposition Congress party has said it will pay the fares.
A statement attributed to the party president Sonia Gandhi said the Congress would make arrangements to pay the fares as a gesture of “solidarity”.
It also questioned why only migrants were being asked to pay fare, when the government had made arrangements to fly back citizens stranded in other countries free of cost.
Thousands fled to their home villages by foot, but many others are still stranded.
The government has defended the move saying it was necessary to ensure that only those who were “really stranded” would use the train services.
Railway Board Chairman VK Yadav told a local newspaper that making the service free would make it difficult to screen people, and that the service was only intended for migrant workers and stranded students.
However, opposition party politicians and civil society members have said it is “inhuman” to expect daily-wage labourers who have not had an income in months, to pay train fare.
Aajeevika Bureau, a non-profit that works with migrant communities, said many of them were simply unable to pay the fares.
It said that in some cases, the cost of a ticket was upwards of 800 (£9; $11) rupees, with some routes asking migrants to also pay a “surcharge”.
Meanwhile, the Stranded Workers Action Network (Swan), which has been operating during the lockdown, has compiled a report based on its interactions with workers, and has said that 50% of them only had rations left for less than a day.
Other findings include the fact that almost half of those who have called them have no food or money and around 80% of them had not received any sort of income since the lockdown began.
This includes those who work in factories and other small industries with many employers either saying they don’t have the funds to pay wages, or simply disappearing altogether.
India’s informal workers are the backbone of the big city economy, constructing houses, cooking food, serving in eateries, delivering takeaways, cutting hair in salons, making automobiles, plumbing toilets and delivering newspapers, among other things.
Most of the estimated 100 million of them live in squalid conditions.
Authorities say the lockdown has been key to saving lives, but critics have said that the lack of planning has hit the country’s poorest and most vulnerable citizens hard.