Prospective passengers started getting "resvn suspended" (reservation suspended) message on railway's website within hours after the flagging off ceremony.
There was some discrepancy in the fare structure which is being rectified by the railway headquarters in Delhi, a senior railway official at Ambala Divisional Headquarters said.
Since the railway website, including online reservation, is controlled by authorities at New Delhi, officials in Punjab could not reveal by when the reservation for the new train would resume.
Earlier a railway official at Chandigarh had told PTI that the snag would be rectified soon, but till late evening the reservation for the new train remained suspended.
Reservation for the new train has also been suspended at various booking offices of the Railways.
Chandigarh is already connected by two Shatabdi Expresses to New Delhi and there has been no disruption in their services.
The new train would run non-stop between the two cities six days a week, except on Sundays.