The ministry has ordered an inquiry into the matter.
"During early hours today after seeing some labourers on track, loco pilot of goods train tried to stop the train but eventually hit them between Badnapur and Karmad stations in Parbhani-Manmad section. Injured have been taken to Aurangabad Civil Hospital. Inquiry has been ordered," the ministry said in a tweet.
Prime Minister Narendra Modi said he had a word with railway minister Piyush Goyal, who is closely monitoring the situation.
"Extremely anguished by the loss of lives due to the rail accident in Aurangabad, Maharashtra. Have spoken to Railway Minister Shri Piyush Goyal and he is closely monitoring the situation. All possible assistance required is being provided," Modi said in a tweet.
The labourers worked in an iron company in Jalna and wanted to catch a special train for Madhya Pradesh.
They had starting walking from Jalna at 7 pm to reach Badnapore and later took the track towards Aurangabad, official spokesperson of the railways said quoting a survivor. After walking for about 36 km, they sat on the railway track to rest and eventually fell asleep. While 14 people sat on the track, two of them sat adjacent to the track and the remaining three were resting at a distance.
The hardship faced by migrant workers has exacerbated amid the nationwide lockdown as they have limited access to basic needs like food and shelter. Millions of migrant labourers have been stranded at their workplace due to the imposition of a nationwide lockdown starting March 25 which also entailed a complete ban on all modes of passenger transport.
Last week, union home ministry allowed Indian Railways to run 'Shramik Special Train' and bus services to help millions of migrant workers, pilgrims, tourists, students and people stranded at different places reach their home states.