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The eight-coach train has seven chair cars, one executive chair car and a total of 600 seats.
The controversy erupted on Saturday after Southern Railway posted a video of the performance on its official X handle.
Television visuals showed students singing the song which is associated with the Rashtriya Swayamsevak Sangh (RSS), during the train journey.
The train's fare is also likely to be on a par with Jan Satabdi fares, sources say.
According to reports, the train's first service might be an inaugural special run.
The fare details for the new Vande Bharat have yet to be announced, but commuters hope it won't be too different from last year's fares.
The catering contracts for Vande Bharat trains would now be invited by the Indian Railway Catering and Tourism Corporation (IRCTC) and not Southern Railway.
The Vande Bharat trains (20632 and 20631) running between Thiruvananthapuram and Mangaluru Central, which stop at Tirur, are often overcrowded.
The train is expected to be launched by mid-November.
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