According to Northern Railway, the train got stalled in the tunnel between Udhampur-Katra section around 5 AM. The tunnel had full ventilation and lighting and there were no safety issues, it said.
A spokesperson said prime facie the cause seems to be wheel slip as there were reports of very heavy rains in the area.
Earlier, railway authorities suspected that the train was stuck due to "engine failure".
The fully air-conditioned super fast train Shri Shakti Express from New Delhi to Katra was on its second run when the incident took place about five kms before the station.
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The train was launched a day earlier from New Delhi.
Meanwhile, Northern Railway has ordered an inquiry into the incident.
A three-member team of officers from Ferozpur Division will inquire into the incident and report at the earliest, the spokesperson said.
Since Katra is a new station from where train services were launched by Prime Minister Narendra Modi recently, another engine was rushed from Udhampur.