This is the second major probe by the fair trade watchdog against a central government enterprise, after Coal India.
The Competition Commission of India's (CCI) latest investigation came on a complaint filed against the Ministry of Railways and the Indian Railway Catering and Tourism Corporation Ltd (IRCTC).
The probe would also look into the possible role of individuals related to the matter.
"The Commission is of the opinion that prima facie, a case of contravention of the provisions of the (Competition) Act is made out against IR (Indian Railways) and IRCTC," the watchdog said in an order made public today.
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Besides, levying premium charges for calls made to 139, which is the railway enquiry service, restricting the services of agents authorised by IRCTC, among others, have also come under the scanner.
"Service charge imposed on e-tickets being non-refundable even if the passenger needed to cancel the ticket; e-wallet scheme with unreasonable conditions appear to be some of their conducts" which have also been found to be prima facie in violation of competition rules.
The DG would also look at the role, if any, of persons in these entities who were responsible for the conduct of the businesses.
"Transportation of passenger through railway in India" appears to be the relevant market in the present case, the order said.
Such a market would also include the ancillary segment like ticketing, catering on board and platform facilities, among others, it added.
The allegations of the three complainants essentially relate to the conduct of Indian Railways with respect to the services provided by its subsidiary IRCTC.